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        Package&nbsp;weblogolib
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<h1 class="epydoc">Source Code for <a href="weblogolib-module.html">Package weblogolib</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno">   1</tt>  <tt class="py-line"><tt class="py-comment">#!/usr/bin/env python</tt> </tt>
<a name="L2"></a><tt class="py-lineno">   2</tt>  <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L3"></a><tt class="py-lineno">   3</tt>  <tt class="py-line"><tt class="py-comment"># -------------------------------- WebLogo --------------------------------</tt> </tt>
<a name="L4"></a><tt class="py-lineno">   4</tt>  <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L5"></a><tt class="py-lineno">   5</tt>  <tt class="py-line"><tt class="py-comment">#  Copyright (c) 2003-2004 The Regents of the University of California.</tt> </tt>
<a name="L6"></a><tt class="py-lineno">   6</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#  Copyright (c) 2005 Gavin E. Crooks</tt> </tt>
<a name="L7"></a><tt class="py-lineno">   7</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#  Copyright (c) 2006-2011, The Regents of the University of California, through </tt> </tt>
<a name="L8"></a><tt class="py-lineno">   8</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#  Lawrence Berkeley National Laboratory (subject to receipt of any required</tt> </tt>
<a name="L9"></a><tt class="py-lineno">   9</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#  approvals from the U.S. Dept. of Energy).  All rights reserved.</tt> </tt>
<a name="L10"></a><tt class="py-lineno">  10</tt>  <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L11"></a><tt class="py-lineno">  11</tt>  <tt class="py-line"><tt class="py-comment">#  This software is distributed under the new BSD Open Source License.</tt> </tt>
<a name="L12"></a><tt class="py-lineno">  12</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#  &lt;http://www.opensource.org/licenses/bsd-license.html&gt;</tt> </tt>
<a name="L13"></a><tt class="py-lineno">  13</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#</tt> </tt>
<a name="L14"></a><tt class="py-lineno">  14</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#  Redistribution and use in source and binary forms, with or without </tt> </tt>
<a name="L15"></a><tt class="py-lineno">  15</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#  modification, are permitted provided that the following conditions are met: </tt> </tt>
<a name="L16"></a><tt class="py-lineno">  16</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#</tt> </tt>
<a name="L17"></a><tt class="py-lineno">  17</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#  (1) Redistributions of source code must retain the above copyright notice, </tt> </tt>
<a name="L18"></a><tt class="py-lineno">  18</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#  this list of conditions and the following disclaimer. </tt> </tt>
<a name="L19"></a><tt class="py-lineno">  19</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#</tt> </tt>
<a name="L20"></a><tt class="py-lineno">  20</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#  (2) Redistributions in binary form must reproduce the above copyright </tt> </tt>
<a name="L21"></a><tt class="py-lineno">  21</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#  notice, this list of conditions and the following disclaimer in the </tt> </tt>
<a name="L22"></a><tt class="py-lineno">  22</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#  documentation and or other materials provided with the distribution. </tt> </tt>
<a name="L23"></a><tt class="py-lineno">  23</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#</tt> </tt>
<a name="L24"></a><tt class="py-lineno">  24</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#  (3) Neither the name of the University of California, Lawrence Berkeley </tt> </tt>
<a name="L25"></a><tt class="py-lineno">  25</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#  National Laboratory, U.S. Dept. of Energy nor the names of its contributors </tt> </tt>
<a name="L26"></a><tt class="py-lineno">  26</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#  may be used to endorse or promote products derived from this software </tt> </tt>
<a name="L27"></a><tt class="py-lineno">  27</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#  without specific prior written permission. </tt> </tt>
<a name="L28"></a><tt class="py-lineno">  28</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#</tt> </tt>
<a name="L29"></a><tt class="py-lineno">  29</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#  THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" </tt> </tt>
<a name="L30"></a><tt class="py-lineno">  30</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#  AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE </tt> </tt>
<a name="L31"></a><tt class="py-lineno">  31</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#  IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE </tt> </tt>
<a name="L32"></a><tt class="py-lineno">  32</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#  ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE </tt> </tt>
<a name="L33"></a><tt class="py-lineno">  33</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#  LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR </tt> </tt>
<a name="L34"></a><tt class="py-lineno">  34</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#  CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF </tt> </tt>
<a name="L35"></a><tt class="py-lineno">  35</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#  SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS </tt> </tt>
<a name="L36"></a><tt class="py-lineno">  36</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#  INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN </tt> </tt>
<a name="L37"></a><tt class="py-lineno">  37</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#  CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) </tt> </tt>
<a name="L38"></a><tt class="py-lineno">  38</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#  ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE </tt> </tt>
<a name="L39"></a><tt class="py-lineno">  39</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#  POSSIBILITY OF SUCH DAMAGE. </tt> </tt>
<a name="L40"></a><tt class="py-lineno">  40</tt>  <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L41"></a><tt class="py-lineno">  41</tt>  <tt class="py-line"><tt class="py-comment"># Replicates README.txt</tt> </tt>
<a name="L42"></a><tt class="py-lineno">  42</tt>  <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L43"></a><tt class="py-lineno">  43</tt>  <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
<a name="L44"></a><tt class="py-lineno">  44</tt>  <tt class="py-line"><tt class="py-docstring">WebLogo (http://code.google.com/p/weblogo/) is a tool for creating sequence </tt> </tt>
<a name="L45"></a><tt class="py-lineno">  45</tt>  <tt class="py-line"><tt class="py-docstring">logos from biological sequence alignments.  It can be run on the command line,</tt> </tt>
<a name="L46"></a><tt class="py-lineno">  46</tt>  <tt class="py-line"><tt class="py-docstring">as a standalone webserver, as a CGI webapp, or as a python library.</tt> </tt>
<a name="L47"></a><tt class="py-lineno">  47</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L48"></a><tt class="py-lineno">  48</tt>  <tt class="py-line"><tt class="py-docstring">The main WebLogo webserver is located at http://weblogo.threeplusone.com</tt> </tt>
<a name="L49"></a><tt class="py-lineno">  49</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L50"></a><tt class="py-lineno">  50</tt>  <tt class="py-line"><tt class="py-docstring">Please consult the manual for installation instructions and more information:</tt> </tt>
<a name="L51"></a><tt class="py-lineno">  51</tt>  <tt class="py-line"><tt class="py-docstring">(Also located in the weblogolib/htdocs subdirectory.)</tt> </tt>
<a name="L52"></a><tt class="py-lineno">  52</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L53"></a><tt class="py-lineno">  53</tt>  <tt class="py-line"><tt class="py-docstring">    http://weblogo.threeplusone.com/manual.html</tt> </tt>
<a name="L54"></a><tt class="py-lineno">  54</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L55"></a><tt class="py-lineno">  55</tt>  <tt class="py-line"><tt class="py-docstring">For help on the command line interface run</tt> </tt>
<a name="L56"></a><tt class="py-lineno">  56</tt>  <tt class="py-line"><tt class="py-docstring">    ./weblogo --help</tt> </tt>
<a name="L57"></a><tt class="py-lineno">  57</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L58"></a><tt class="py-lineno">  58</tt>  <tt class="py-line"><tt class="py-docstring">To build a simple logo run</tt> </tt>
<a name="L59"></a><tt class="py-lineno">  59</tt>  <tt class="py-line"><tt class="py-docstring">    ./weblogo  &lt; cap.fa &gt; logo0.eps</tt> </tt>
<a name="L60"></a><tt class="py-lineno">  60</tt>  <tt class="py-line"><tt class="py-docstring">    </tt> </tt>
<a name="L61"></a><tt class="py-lineno">  61</tt>  <tt class="py-line"><tt class="py-docstring">To run as a standalone webserver at localhost:8080 </tt> </tt>
<a name="L62"></a><tt class="py-lineno">  62</tt>  <tt class="py-line"><tt class="py-docstring">    ./weblogo --serve</tt> </tt>
<a name="L63"></a><tt class="py-lineno">  63</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L64"></a><tt class="py-lineno">  64</tt>  <tt class="py-line"><tt class="py-docstring">To create a logo in python code:</tt> </tt>
<a name="L65"></a><tt class="py-lineno">  65</tt>  <tt class="py-line"><tt class="py-docstring">    &gt;&gt;&gt; from weblogolib import *</tt> </tt>
<a name="L66"></a><tt class="py-lineno">  66</tt>  <tt class="py-line"><tt class="py-docstring">    &gt;&gt;&gt; fin = open('cap.fa')</tt> </tt>
<a name="L67"></a><tt class="py-lineno">  67</tt>  <tt class="py-line"><tt class="py-docstring">    &gt;&gt;&gt; seqs = read_seq_data(fin) </tt> </tt>
<a name="L68"></a><tt class="py-lineno">  68</tt>  <tt class="py-line"><tt class="py-docstring">    &gt;&gt;&gt; data = LogoData.from_seqs(seqs)</tt> </tt>
<a name="L69"></a><tt class="py-lineno">  69</tt>  <tt class="py-line"><tt class="py-docstring">    &gt;&gt;&gt; options = LogoOptions()</tt> </tt>
<a name="L70"></a><tt class="py-lineno">  70</tt>  <tt class="py-line"><tt class="py-docstring">    &gt;&gt;&gt; options.title = "A Logo Title"</tt> </tt>
<a name="L71"></a><tt class="py-lineno">  71</tt>  <tt class="py-line"><tt class="py-docstring">    &gt;&gt;&gt; format = LogoFormat(data, options)</tt> </tt>
<a name="L72"></a><tt class="py-lineno">  72</tt>  <tt class="py-line"><tt class="py-docstring">    &gt;&gt;&gt; fout = open('cap.eps', 'w') </tt> </tt>
<a name="L73"></a><tt class="py-lineno">  73</tt>  <tt class="py-line"><tt class="py-docstring">    &gt;&gt;&gt; eps_formatter( data, format, fout)</tt> </tt>
<a name="L74"></a><tt class="py-lineno">  74</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L75"></a><tt class="py-lineno">  75</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L76"></a><tt class="py-lineno">  76</tt>  <tt class="py-line"><tt class="py-docstring">-- Distribution and Modification --</tt> </tt>
<a name="L77"></a><tt class="py-lineno">  77</tt>  <tt class="py-line"><tt class="py-docstring">This package is distributed under the new BSD Open Source License. </tt> </tt>
<a name="L78"></a><tt class="py-lineno">  78</tt>  <tt class="py-line"><tt class="py-docstring">Please see the LICENSE.txt file for details on copyright and licensing.</tt> </tt>
<a name="L79"></a><tt class="py-lineno">  79</tt>  <tt class="py-line"><tt class="py-docstring">The WebLogo source code can be downloaded from </tt> </tt>
<a name="L80"></a><tt class="py-lineno">  80</tt>  <tt class="py-line"><tt class="py-docstring">http://code.google.com/p/weblogo/</tt> </tt>
<a name="L81"></a><tt class="py-lineno">  81</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L82"></a><tt class="py-lineno">  82</tt>  <tt class="py-line"><tt class="py-docstring">WebLogo requires Python 2.5, 2.6 or 2.7, and the python</tt> </tt>
<a name="L83"></a><tt class="py-lineno">  83</tt>  <tt class="py-line"><tt class="py-docstring">array package 'numpy' (http://www.scipy.org/Download)</tt> </tt>
<a name="L84"></a><tt class="py-lineno">  84</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L85"></a><tt class="py-lineno">  85</tt>  <tt class="py-line"><tt class="py-docstring">Generating logos in PDF or bitmap graphics formats require that the ghostscript</tt> </tt>
<a name="L86"></a><tt class="py-lineno">  86</tt>  <tt class="py-line"><tt class="py-docstring">program 'gs' be installed. Scalable Vector Graphics (SVG) format also requires </tt> </tt>
<a name="L87"></a><tt class="py-lineno">  87</tt>  <tt class="py-line"><tt class="py-docstring">the program 'pdf2svg'.</tt> </tt>
<a name="L88"></a><tt class="py-lineno">  88</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L89"></a><tt class="py-lineno">  89</tt>  <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
<a name="L90"></a><tt class="py-lineno">  90</tt>  <tt class="py-line"> </tt>
<a name="L91"></a><tt class="py-lineno">  91</tt>  <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">sys</tt> </tt>
<a name="L92"></a><tt class="py-lineno">  92</tt>  <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">copy</tt> </tt>
<a name="L93"></a><tt class="py-lineno">  93</tt>  <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">os</tt> </tt>
<a name="L94"></a><tt class="py-lineno">  94</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">datetime</tt> <tt class="py-keyword">import</tt> <tt class="py-name">datetime</tt> </tt>
<a name="L95"></a><tt class="py-lineno">  95</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">StringIO</tt> <tt class="py-keyword">import</tt> <tt class="py-name">StringIO</tt> </tt>
<a name="L96"></a><tt class="py-lineno">  96</tt>  <tt class="py-line"> </tt>
<a name="L97"></a><tt class="py-lineno">  97</tt>  <tt class="py-line"><tt class="py-keyword">from</tt>  <tt class="py-name">corebio</tt><tt class="py-op">.</tt><tt class="py-name">data</tt> <tt class="py-keyword">import</tt> <tt class="py-name">rna_letters</tt><tt class="py-op">,</tt> <tt class="py-name">dna_letters</tt><tt class="py-op">,</tt> <tt class="py-name">amino_acid_letters</tt> </tt>
<a name="L98"></a><tt class="py-lineno">  98</tt>  <tt class="py-line"> </tt>
<a name="L99"></a><tt class="py-lineno">  99</tt>  <tt class="py-line"> </tt>
<a name="L100"></a><tt class="py-lineno"> 100</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">string</tt> <tt class="py-keyword">import</tt> <tt class="py-name">Template</tt> </tt>
<a name="L101"></a><tt class="py-lineno"> 101</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">subprocess</tt> <tt class="py-keyword">import</tt> <tt class="py-op">*</tt> </tt>
<a name="L102"></a><tt class="py-lineno"> 102</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">corebio</tt><tt class="py-op">.</tt><tt class="py-name">utils</tt> <tt class="py-keyword">import</tt> <tt id="link-0" class="py-name" targets="Function weblogolib._cgi.resource_string()=weblogolib._cgi-module.html#resource_string"><a title="weblogolib._cgi.resource_string" class="py-name" href="#" onclick="return doclink('link-0', 'resource_string', 'link-0');">resource_string</a></tt><tt class="py-op">,</tt> <tt class="py-name">resource_filename</tt> </tt>
<a name="L103"></a><tt class="py-lineno"> 103</tt>  <tt class="py-line"> </tt>
<a name="L104"></a><tt class="py-lineno"> 104</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">math</tt> <tt class="py-keyword">import</tt> <tt class="py-name">log</tt><tt class="py-op">,</tt> <tt class="py-name">sqrt</tt><tt class="py-op">,</tt> <tt class="py-name">exp</tt> </tt>
<a name="L105"></a><tt class="py-lineno"> 105</tt>  <tt class="py-line"> </tt>
<a name="L106"></a><tt class="py-lineno"> 106</tt>  <tt class="py-line"><tt class="py-comment"># Avoid 'from numpy import *' since numpy has lots of names defined</tt> </tt>
<a name="L107"></a><tt class="py-lineno"> 107</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-keyword">from</tt> <tt class="py-name">numpy</tt> <tt class="py-keyword">import</tt> <tt class="py-name">array</tt><tt class="py-op">,</tt> <tt class="py-name">asarray</tt><tt class="py-op">,</tt> <tt class="py-name">float64</tt><tt class="py-op">,</tt> <tt class="py-name">ones</tt><tt class="py-op">,</tt> <tt class="py-name">zeros</tt><tt class="py-op">,</tt> <tt class="py-name">int32</tt><tt class="py-op">,</tt><tt class="py-name">all</tt><tt class="py-op">,</tt><tt class="py-name">any</tt><tt class="py-op">,</tt> <tt class="py-name">shape</tt> </tt>
<a name="L108"></a><tt class="py-lineno"> 108</tt>  <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">numpy</tt> <tt class="py-name">as</tt> <tt class="py-name">na</tt> </tt>
<a name="L109"></a><tt class="py-lineno"> 109</tt>  <tt class="py-line"> </tt>
<a name="L110"></a><tt class="py-lineno"> 110</tt>  <tt class="py-line"> </tt>
<a name="L111"></a><tt class="py-lineno"> 111</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-1" class="py-name" targets="Module weblogolib.color=weblogolib.color-module.html,Method weblogolib.colorscheme.ColorScheme.color()=weblogolib.colorscheme.ColorScheme-class.html#color"><a title="weblogolib.color
weblogolib.colorscheme.ColorScheme.color" class="py-name" href="#" onclick="return doclink('link-1', 'color', 'link-1');">color</a></tt> <tt class="py-keyword">import</tt> <tt class="py-op">*</tt> </tt>
<a name="L112"></a><tt class="py-lineno"> 112</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-2" class="py-name" targets="Module weblogolib.colorscheme=weblogolib.colorscheme-module.html"><a title="weblogolib.colorscheme" class="py-name" href="#" onclick="return doclink('link-2', 'colorscheme', 'link-2');">colorscheme</a></tt> <tt class="py-keyword">import</tt> <tt class="py-op">*</tt> </tt>
<a name="L113"></a><tt class="py-lineno"> 113</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">corebio</tt><tt class="py-op">.</tt><tt class="py-name">seq</tt> <tt class="py-keyword">import</tt> <tt class="py-name">Alphabet</tt><tt class="py-op">,</tt> <tt class="py-name">Seq</tt><tt class="py-op">,</tt> <tt class="py-name">SeqList</tt> </tt>
<a name="L114"></a><tt class="py-lineno"> 114</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">corebio</tt> <tt class="py-keyword">import</tt> <tt class="py-name">seq_io</tt> </tt>
<a name="L115"></a><tt class="py-lineno"> 115</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">corebio</tt><tt class="py-op">.</tt><tt class="py-name">utils</tt> <tt class="py-keyword">import</tt> <tt class="py-name">isfloat</tt><tt class="py-op">,</tt> <tt class="py-name">find_command</tt><tt class="py-op">,</tt> <tt class="py-name">ArgumentError</tt><tt class="py-op">,</tt> <tt class="py-name">stdrepr</tt> </tt>
<a name="L116"></a><tt class="py-lineno"> 116</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">corebio</tt><tt class="py-op">.</tt><tt class="py-name">moremath</tt> <tt class="py-keyword">import</tt> <tt class="py-op">*</tt> </tt>
<a name="L117"></a><tt class="py-lineno"> 117</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">corebio</tt><tt class="py-op">.</tt><tt class="py-name">data</tt> <tt class="py-keyword">import</tt> <tt class="py-name">amino_acid_composition</tt> </tt>
<a name="L118"></a><tt class="py-lineno"> 118</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">corebio</tt><tt class="py-op">.</tt><tt class="py-name">seq</tt> <tt class="py-keyword">import</tt> <tt class="py-name">unambiguous_rna_alphabet</tt><tt class="py-op">,</tt> <tt class="py-name">unambiguous_dna_alphabet</tt><tt class="py-op">,</tt> <tt class="py-name">unambiguous_protein_alphabet</tt> </tt>
<a name="L119"></a><tt class="py-lineno"> 119</tt>  <tt class="py-line"> </tt>
<a name="L120"></a><tt class="py-lineno"> 120</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-3" class="py-name" targets="Module weblogolib.logomath=weblogolib.logomath-module.html"><a title="weblogolib.logomath" class="py-name" href="#" onclick="return doclink('link-3', 'logomath', 'link-3');">logomath</a></tt> <tt class="py-keyword">import</tt> <tt id="link-4" class="py-name" targets="Class weblogolib.logomath.Dirichlet=weblogolib.logomath.Dirichlet-class.html"><a title="weblogolib.logomath.Dirichlet" class="py-name" href="#" onclick="return doclink('link-4', 'Dirichlet', 'link-4');">Dirichlet</a></tt> </tt>
<a name="L121"></a><tt class="py-lineno"> 121</tt>  <tt class="py-line"> </tt>
<a name="L122"></a><tt class="py-lineno"> 122</tt>  <tt class="py-line"> </tt>
<a name="L123"></a><tt class="py-lineno"> 123</tt>  <tt class="py-line"><tt class="py-comment"># ------ META DATA ------</tt> </tt>
<a name="L124"></a><tt class="py-lineno"> 124</tt>  <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L125"></a><tt class="py-lineno"> 125</tt>  <tt class="py-line"><tt class="py-name">__all__</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt> <tt class="py-string">'LogoOptions'</tt><tt class="py-op">,</tt>  </tt>
<a name="L126"></a><tt class="py-lineno"> 126</tt>  <tt class="py-line">            <tt class="py-string">'description'</tt><tt class="py-op">,</tt>  </tt>
<a name="L127"></a><tt class="py-lineno"> 127</tt>  <tt class="py-line">            <tt class="py-string">'__version__'</tt><tt class="py-op">,</tt>  </tt>
<a name="L128"></a><tt class="py-lineno"> 128</tt>  <tt class="py-line">            <tt class="py-string">'LogoFormat'</tt><tt class="py-op">,</tt> </tt>
<a name="L129"></a><tt class="py-lineno"> 129</tt>  <tt class="py-line">            <tt class="py-string">'LogoData'</tt><tt class="py-op">,</tt> </tt>
<a name="L130"></a><tt class="py-lineno"> 130</tt>  <tt class="py-line">            <tt class="py-string">'GhostscriptAPI'</tt><tt class="py-op">,</tt> </tt>
<a name="L131"></a><tt class="py-lineno"> 131</tt>  <tt class="py-line">            <tt class="py-string">'std_color_schemes'</tt><tt class="py-op">,</tt> </tt>
<a name="L132"></a><tt class="py-lineno"> 132</tt>  <tt class="py-line">            <tt class="py-string">'default_color_schemes'</tt><tt class="py-op">,</tt> </tt>
<a name="L133"></a><tt class="py-lineno"> 133</tt>  <tt class="py-line">            <tt class="py-string">'classic'</tt><tt class="py-op">,</tt> </tt>
<a name="L134"></a><tt class="py-lineno"> 134</tt>  <tt class="py-line">            <tt class="py-string">'std_units'</tt><tt class="py-op">,</tt> </tt>
<a name="L135"></a><tt class="py-lineno"> 135</tt>  <tt class="py-line">            <tt class="py-string">'std_sizes'</tt><tt class="py-op">,</tt> </tt>
<a name="L136"></a><tt class="py-lineno"> 136</tt>  <tt class="py-line">            <tt class="py-string">'std_alphabets'</tt><tt class="py-op">,</tt> </tt>
<a name="L137"></a><tt class="py-lineno"> 137</tt>  <tt class="py-line">            <tt class="py-string">'std_percentCG'</tt><tt class="py-op">,</tt> </tt>
<a name="L138"></a><tt class="py-lineno"> 138</tt>  <tt class="py-line">            <tt class="py-string">'pdf_formatter'</tt><tt class="py-op">,</tt> </tt>
<a name="L139"></a><tt class="py-lineno"> 139</tt>  <tt class="py-line">            <tt class="py-string">'jpeg_formatter'</tt><tt class="py-op">,</tt> </tt>
<a name="L140"></a><tt class="py-lineno"> 140</tt>  <tt class="py-line">            <tt class="py-string">'png_formatter'</tt><tt class="py-op">,</tt> </tt>
<a name="L141"></a><tt class="py-lineno"> 141</tt>  <tt class="py-line">            <tt class="py-string">'png_print_formatter'</tt><tt class="py-op">,</tt> </tt>
<a name="L142"></a><tt class="py-lineno"> 142</tt>  <tt class="py-line">            <tt class="py-string">'txt_formatter'</tt><tt class="py-op">,</tt> </tt>
<a name="L143"></a><tt class="py-lineno"> 143</tt>  <tt class="py-line">            <tt class="py-string">'eps_formatter'</tt><tt class="py-op">,</tt> </tt>
<a name="L144"></a><tt class="py-lineno"> 144</tt>  <tt class="py-line">            <tt class="py-string">'formatters'</tt><tt class="py-op">,</tt> </tt>
<a name="L145"></a><tt class="py-lineno"> 145</tt>  <tt class="py-line">            <tt class="py-string">'default_formatter'</tt><tt class="py-op">,</tt> </tt>
<a name="L146"></a><tt class="py-lineno"> 146</tt>  <tt class="py-line">            <tt class="py-string">'base_distribution'</tt><tt class="py-op">,</tt> </tt>
<a name="L147"></a><tt class="py-lineno"> 147</tt>  <tt class="py-line">            <tt class="py-string">'equiprobable_distribution'</tt><tt class="py-op">,</tt> </tt>
<a name="L148"></a><tt class="py-lineno"> 148</tt>  <tt class="py-line">            <tt class="py-string">'read_seq_data'</tt><tt class="py-op">,</tt> </tt>
<a name="L149"></a><tt class="py-lineno"> 149</tt>  <tt class="py-line">            <tt class="py-string">'color'</tt><tt class="py-op">,</tt> </tt>
<a name="L150"></a><tt class="py-lineno"> 150</tt>  <tt class="py-line">            <tt class="py-string">'colorscheme'</tt><tt class="py-op">,</tt> </tt>
<a name="L151"></a><tt class="py-lineno"> 151</tt>  <tt class="py-line">            <tt class="py-string">'logomath'</tt><tt class="py-op">,</tt> </tt>
<a name="L152"></a><tt class="py-lineno"> 152</tt>  <tt class="py-line">            <tt class="py-op">]</tt> </tt>
<a name="L153"></a><tt class="py-lineno"> 153</tt>  <tt class="py-line"> </tt>
<a name="L154"></a><tt class="py-lineno"> 154</tt>  <tt class="py-line"><tt id="link-5" class="py-name" targets="Variable weblogolib.description=weblogolib-module.html#description"><a title="weblogolib.description" class="py-name" href="#" onclick="return doclink('link-5', 'description', 'link-5');">description</a></tt>  <tt class="py-op">=</tt> <tt class="py-string">"Create sequence logos from biological sequence alignments."</tt>  </tt>
<a name="L155"></a><tt class="py-lineno"> 155</tt>  <tt class="py-line"> </tt>
<a name="L156"></a><tt class="py-lineno"> 156</tt>  <tt class="py-line"><tt class="py-name">__version__</tt> <tt class="py-op">=</tt> <tt class="py-string">"3.2"</tt> </tt>
<a name="L157"></a><tt class="py-lineno"> 157</tt>  <tt class="py-line"> </tt>
<a name="L158"></a><tt class="py-lineno"> 158</tt>  <tt class="py-line"><tt class="py-comment"># These keywords are substituted by subversion .</tt> </tt>
<a name="L159"></a><tt class="py-lineno"> 159</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># The date and revision will only tell the truth after a branch or tag,</tt> </tt>
<a name="L160"></a><tt class="py-lineno"> 160</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># since different files in trunk will have been changed at different times</tt> </tt>
<a name="L161"></a><tt class="py-lineno"> 161</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt id="link-6" class="py-name" targets="Variable weblogolib.release_date=weblogolib-module.html#release_date"><a title="weblogolib.release_date" class="py-name" href="#" onclick="return doclink('link-6', 'release_date', 'link-6');">release_date</a></tt> <tt class="py-op">=</tt><tt class="py-string">"$Date: 2011-11-07 19:14:18 -0800 (Mon, 07 Nov 2011) $"</tt><tt class="py-op">.</tt><tt class="py-name">split</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L162"></a><tt class="py-lineno"> 162</tt>  <tt class="py-line"><tt id="link-7" class="py-name" targets="Variable weblogolib.release_build=weblogolib-module.html#release_build"><a title="weblogolib.release_build" class="py-name" href="#" onclick="return doclink('link-7', 'release_build', 'link-7');">release_build</a></tt> <tt class="py-op">=</tt> <tt class="py-string">"$Revision: 118 $"</tt><tt class="py-op">.</tt><tt class="py-name">split</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L163"></a><tt class="py-lineno"> 163</tt>  <tt class="py-line"><tt id="link-8" class="py-name" targets="Variable weblogolib.release_description=weblogolib-module.html#release_description"><a title="weblogolib.release_description" class="py-name" href="#" onclick="return doclink('link-8', 'release_description', 'link-8');">release_description</a></tt> <tt class="py-op">=</tt> <tt class="py-string">"WebLogo %s (%s)"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">__version__</tt><tt class="py-op">,</tt>  <tt id="link-9" class="py-name"><a title="weblogolib.release_date" class="py-name" href="#" onclick="return doclink('link-9', 'release_date', 'link-6');">release_date</a></tt><tt class="py-op">)</tt> </tt>
<a name="cgi"></a><div id="cgi-def"><a name="L164"></a><tt class="py-lineno"> 164</tt>  <tt class="py-line"> </tt>
<a name="L165"></a><tt class="py-lineno"> 165</tt>  <tt class="py-line"> </tt>
<a name="L166"></a><tt class="py-lineno"> 166</tt>  <tt class="py-line"> </tt>
<a name="L167"></a><tt class="py-lineno"> 167</tt> <a class="py-toggle" href="#" id="cgi-toggle" onclick="return toggle('cgi');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="weblogolib-module.html#cgi">cgi</a><tt class="py-op">(</tt><tt class="py-param">htdocs_directory</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
</div><div id="cgi-collapsed" style="display:none;" pad="++++" indent="++++"></div><div id="cgi-expanded"><a name="L168"></a><tt class="py-lineno"> 168</tt>  <tt class="py-line">    <tt class="py-keyword">import</tt> <tt id="link-10" class="py-name" targets="Package weblogolib=weblogolib-module.html"><a title="weblogolib" class="py-name" href="#" onclick="return doclink('link-10', 'weblogolib', 'link-10');">weblogolib</a></tt><tt class="py-op">.</tt><tt id="link-11" class="py-name" targets="Module weblogolib._cgi=weblogolib._cgi-module.html"><a title="weblogolib._cgi" class="py-name" href="#" onclick="return doclink('link-11', '_cgi', 'link-11');">_cgi</a></tt> </tt>
<a name="L169"></a><tt class="py-lineno"> 169</tt>  <tt class="py-line">    <tt id="link-12" class="py-name"><a title="weblogolib" class="py-name" href="#" onclick="return doclink('link-12', 'weblogolib', 'link-10');">weblogolib</a></tt><tt class="py-op">.</tt><tt id="link-13" class="py-name"><a title="weblogolib._cgi" class="py-name" href="#" onclick="return doclink('link-13', '_cgi', 'link-11');">_cgi</a></tt><tt class="py-op">.</tt><tt id="link-14" class="py-name" targets="Function weblogolib._cgi.main()=weblogolib._cgi-module.html#main,Function weblogolib._cli.main()=weblogolib._cli-module.html#main"><a title="weblogolib._cgi.main
weblogolib._cli.main" class="py-name" href="#" onclick="return doclink('link-14', 'main', 'link-14');">main</a></tt><tt class="py-op">(</tt><tt class="py-name">htdocs_directory</tt><tt class="py-op">)</tt> </tt>
</div><a name="L170"></a><tt class="py-lineno"> 170</tt>  <tt class="py-line">         </tt>
<a name="GhostscriptAPI"></a><div id="GhostscriptAPI-def"><a name="L171"></a><tt class="py-lineno"> 171</tt> <a class="py-toggle" href="#" id="GhostscriptAPI-toggle" onclick="return toggle('GhostscriptAPI');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="weblogolib.GhostscriptAPI-class.html">GhostscriptAPI</a><tt class="py-op">(</tt><tt class="py-base-class">object</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
</div><div id="GhostscriptAPI-collapsed" style="display:none;" pad="++++" indent="++++"></div><div id="GhostscriptAPI-expanded"><a name="L172"></a><tt class="py-lineno"> 172</tt>  <tt class="py-line">    <tt class="py-docstring">"""Interface to the command line program Ghostscript ('gs')"""</tt> </tt>
<a name="L173"></a><tt class="py-lineno"> 173</tt>  <tt class="py-line">     </tt>
<a name="L174"></a><tt class="py-lineno"> 174</tt>  <tt class="py-line">    <tt id="link-15" class="py-name" targets="Variable weblogolib.GhostscriptAPI.formats=weblogolib.GhostscriptAPI-class.html#formats"><a title="weblogolib.GhostscriptAPI.formats" class="py-name" href="#" onclick="return doclink('link-15', 'formats', 'link-15');">formats</a></tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-string">'png'</tt><tt class="py-op">,</tt> <tt class="py-string">'pdf'</tt><tt class="py-op">,</tt> <tt class="py-string">'jpeg'</tt><tt class="py-op">)</tt> </tt>
<a name="L175"></a><tt class="py-lineno"> 175</tt>  <tt class="py-line">     </tt>
<a name="GhostscriptAPI.__init__"></a><div id="GhostscriptAPI.__init__-def"><a name="L176"></a><tt class="py-lineno"> 176</tt> <a class="py-toggle" href="#" id="GhostscriptAPI.__init__-toggle" onclick="return toggle('GhostscriptAPI.__init__');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="weblogolib.GhostscriptAPI-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">path</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
</div><div id="GhostscriptAPI.__init__-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="GhostscriptAPI.__init__-expanded"><a name="L177"></a><tt class="py-lineno"> 177</tt>  <tt class="py-line">        <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L178"></a><tt class="py-lineno"> 178</tt>  <tt class="py-line">            <tt class="py-name">command</tt> <tt class="py-op">=</tt> <tt class="py-name">find_command</tt><tt class="py-op">(</tt><tt class="py-string">'gs'</tt><tt class="py-op">,</tt> <tt class="py-name">path</tt><tt class="py-op">=</tt><tt class="py-name">path</tt><tt class="py-op">)</tt> </tt>
<a name="L179"></a><tt class="py-lineno"> 179</tt>  <tt class="py-line">        <tt class="py-keyword">except</tt> <tt class="py-name">EnvironmentError</tt><tt class="py-op">:</tt> </tt>
<a name="L180"></a><tt class="py-lineno"> 180</tt>  <tt class="py-line">            <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L181"></a><tt class="py-lineno"> 181</tt>  <tt class="py-line">                <tt class="py-name">command</tt> <tt class="py-op">=</tt> <tt class="py-name">find_command</tt><tt class="py-op">(</tt><tt class="py-string">'gswin32c.exe'</tt><tt class="py-op">,</tt> <tt class="py-name">path</tt><tt class="py-op">=</tt><tt class="py-name">path</tt><tt class="py-op">)</tt> </tt>
<a name="L182"></a><tt class="py-lineno"> 182</tt>  <tt class="py-line">            <tt class="py-keyword">except</tt> <tt class="py-name">EnvironmentError</tt><tt class="py-op">:</tt> </tt>
<a name="L183"></a><tt class="py-lineno"> 183</tt>  <tt class="py-line">                <tt class="py-keyword">raise</tt> <tt class="py-name">EnvironmentError</tt><tt class="py-op">(</tt><tt class="py-string">"Could not find Ghostscript on path."</tt> </tt>
<a name="L184"></a><tt class="py-lineno"> 184</tt>  <tt class="py-line">                <tt class="py-string">" There should be either a gs executable or a gswin32c.exe on your system's path"</tt><tt class="py-op">)</tt> </tt>
<a name="L185"></a><tt class="py-lineno"> 185</tt>  <tt class="py-line">         </tt>
<a name="L186"></a><tt class="py-lineno"> 186</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">command</tt> <tt class="py-op">=</tt> <tt class="py-name">command</tt>         </tt>
</div><a name="L187"></a><tt class="py-lineno"> 187</tt>  <tt class="py-line">     </tt>
<a name="GhostscriptAPI.version"></a><div id="GhostscriptAPI.version-def"><a name="L188"></a><tt class="py-lineno"> 188</tt> <a class="py-toggle" href="#" id="GhostscriptAPI.version-toggle" onclick="return toggle('GhostscriptAPI.version');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="weblogolib.GhostscriptAPI-class.html#version">version</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
</div><div id="GhostscriptAPI.version-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="GhostscriptAPI.version-expanded"><a name="L189"></a><tt class="py-lineno"> 189</tt>  <tt class="py-line">        <tt class="py-name">args</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">command</tt><tt class="py-op">,</tt> <tt class="py-string">'--version'</tt><tt class="py-op">]</tt> </tt>
<a name="L190"></a><tt class="py-lineno"> 190</tt>  <tt class="py-line">        <tt class="py-keyword">try</tt> <tt class="py-op">:</tt> </tt>
<a name="L191"></a><tt class="py-lineno"> 191</tt>  <tt class="py-line">            <tt class="py-name">p</tt> <tt class="py-op">=</tt> <tt class="py-name">Popen</tt><tt class="py-op">(</tt><tt class="py-name">args</tt><tt class="py-op">,</tt> <tt class="py-name">stdout</tt><tt class="py-op">=</tt><tt class="py-name">PIPE</tt><tt class="py-op">)</tt> </tt>
<a name="L192"></a><tt class="py-lineno"> 192</tt>  <tt class="py-line">            <tt class="py-op">(</tt><tt class="py-name">out</tt><tt class="py-op">,</tt><tt class="py-name">err</tt><tt class="py-op">)</tt> <tt class="py-op">=</tt> <tt class="py-name">p</tt><tt class="py-op">.</tt><tt class="py-name">communicate</tt><tt class="py-op">(</tt><tt class="py-op">)</tt>  </tt>
<a name="L193"></a><tt class="py-lineno"> 193</tt>  <tt class="py-line">        <tt class="py-keyword">except</tt> <tt class="py-name">OSError</tt> <tt class="py-op">:</tt> </tt>
<a name="L194"></a><tt class="py-lineno"> 194</tt>  <tt class="py-line">            <tt class="py-keyword">raise</tt> <tt class="py-name">RuntimeError</tt><tt class="py-op">(</tt><tt class="py-string">"Cannot communicate with ghostscript."</tt><tt class="py-op">)</tt>   </tt>
<a name="L195"></a><tt class="py-lineno"> 195</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">out</tt><tt class="py-op">.</tt><tt class="py-name">strip</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L196"></a><tt class="py-lineno"> 196</tt>  <tt class="py-line">        </tt>
<a name="GhostscriptAPI.convert"></a><div id="GhostscriptAPI.convert-def"><a name="L197"></a><tt class="py-lineno"> 197</tt> <a class="py-toggle" href="#" id="GhostscriptAPI.convert-toggle" onclick="return toggle('GhostscriptAPI.convert');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="weblogolib.GhostscriptAPI-class.html#convert">convert</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">format</tt><tt class="py-op">,</tt> <tt class="py-param">fin</tt><tt class="py-op">,</tt> <tt class="py-param">fout</tt><tt class="py-op">,</tt>  <tt class="py-param">width</tt><tt class="py-op">,</tt>  <tt class="py-param">height</tt><tt class="py-op">,</tt> <tt class="py-param">resolution</tt><tt class="py-op">=</tt><tt class="py-number">300</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
</div><div id="GhostscriptAPI.convert-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="GhostscriptAPI.convert-expanded"><a name="L198"></a><tt class="py-lineno"> 198</tt>  <tt class="py-line">        <tt class="py-name">device_map</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt> <tt class="py-string">'png'</tt><tt class="py-op">:</tt><tt class="py-string">'png16m'</tt><tt class="py-op">,</tt>  <tt class="py-string">'pdf'</tt><tt class="py-op">:</tt><tt class="py-string">'pdfwrite'</tt><tt class="py-op">,</tt> <tt class="py-string">'jpeg'</tt><tt class="py-op">:</tt><tt class="py-string">'jpeg'</tt><tt class="py-op">}</tt> </tt>
<a name="L199"></a><tt class="py-lineno"> 199</tt>  <tt class="py-line">        </tt>
<a name="L200"></a><tt class="py-lineno"> 200</tt>  <tt class="py-line">        <tt class="py-keyword">try</tt> <tt class="py-op">:</tt> </tt>
<a name="L201"></a><tt class="py-lineno"> 201</tt>  <tt class="py-line">            <tt class="py-name">device</tt> <tt class="py-op">=</tt> <tt class="py-name">device_map</tt><tt class="py-op">[</tt><tt class="py-name">format</tt><tt class="py-op">]</tt> </tt>
<a name="L202"></a><tt class="py-lineno"> 202</tt>  <tt class="py-line">        <tt class="py-keyword">except</tt> <tt class="py-name">KeyError</tt><tt class="py-op">:</tt> </tt>
<a name="L203"></a><tt class="py-lineno"> 203</tt>  <tt class="py-line">            <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">(</tt><tt class="py-string">"Unsupported format."</tt><tt class="py-op">)</tt> </tt>
<a name="L204"></a><tt class="py-lineno"> 204</tt>  <tt class="py-line">         </tt>
<a name="L205"></a><tt class="py-lineno"> 205</tt>  <tt class="py-line">        <tt class="py-name">args</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">command</tt><tt class="py-op">,</tt>  </tt>
<a name="L206"></a><tt class="py-lineno"> 206</tt>  <tt class="py-line">            <tt class="py-string">"-sDEVICE=%s"</tt> <tt class="py-op">%</tt> <tt class="py-name">device</tt><tt class="py-op">,</tt>  </tt>
<a name="L207"></a><tt class="py-lineno"> 207</tt>  <tt class="py-line">            <tt class="py-string">"-dPDFSETTINGS=/printer"</tt><tt class="py-op">,</tt> </tt>
<a name="L208"></a><tt class="py-lineno"> 208</tt>  <tt class="py-line">            <tt class="py-comment">#"-q",   # Quite: Do not dump messages to stdout.</tt> </tt>
<a name="L209"></a><tt class="py-lineno"> 209</tt>  <tt class="py-line">            <tt class="py-string">"-sstdout=%stderr"</tt><tt class="py-op">,</tt> <tt class="py-comment"># Redirect messages and errors to stderr</tt> </tt>
<a name="L210"></a><tt class="py-lineno"> 210</tt>  <tt class="py-line">            <tt class="py-string">"-sOutputFile=-"</tt><tt class="py-op">,</tt> <tt class="py-comment"># Stdout</tt> </tt>
<a name="L211"></a><tt class="py-lineno"> 211</tt>  <tt class="py-line">            <tt class="py-string">"-dDEVICEWIDTHPOINTS=%s"</tt> <tt class="py-op">%</tt> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">width</tt><tt class="py-op">)</tt><tt class="py-op">,</tt>   </tt>
<a name="L212"></a><tt class="py-lineno"> 212</tt>  <tt class="py-line">            <tt class="py-string">"-dDEVICEHEIGHTPOINTS=%s"</tt> <tt class="py-op">%</tt> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">height</tt><tt class="py-op">)</tt><tt class="py-op">,</tt>   </tt>
<a name="L213"></a><tt class="py-lineno"> 213</tt>  <tt class="py-line">            <tt class="py-string">"-dSAFER"</tt><tt class="py-op">,</tt>  <tt class="py-comment"># For added security</tt> </tt>
<a name="L214"></a><tt class="py-lineno"> 214</tt>  <tt class="py-line">            <tt class="py-string">"-dNOPAUSE"</tt><tt class="py-op">,</tt><tt class="py-op">]</tt> </tt>
<a name="L215"></a><tt class="py-lineno"> 215</tt>  <tt class="py-line">             </tt>
<a name="L216"></a><tt class="py-lineno"> 216</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">device</tt> <tt class="py-op">!=</tt> <tt class="py-string">'pdf'</tt> <tt class="py-op">:</tt> </tt>
<a name="L217"></a><tt class="py-lineno"> 217</tt>  <tt class="py-line">            <tt class="py-name">args</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-string">"-r%s"</tt> <tt class="py-op">%</tt> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">resolution</tt><tt class="py-op">)</tt> <tt class="py-op">)</tt>  </tt>
<a name="L218"></a><tt class="py-lineno"> 218</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">resolution</tt> <tt class="py-op">&lt;</tt> <tt class="py-number">300</tt> <tt class="py-op">:</tt> <tt class="py-comment"># Antialias if resolution is Less than 300 DPI</tt> </tt>
<a name="L219"></a><tt class="py-lineno"> 219</tt>  <tt class="py-line">                <tt class="py-name">args</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-string">"-dGraphicsAlphaBits=4"</tt><tt class="py-op">)</tt> </tt>
<a name="L220"></a><tt class="py-lineno"> 220</tt>  <tt class="py-line">                <tt class="py-name">args</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-string">"-dTextAlphaBits=4"</tt><tt class="py-op">)</tt> </tt>
<a name="L221"></a><tt class="py-lineno"> 221</tt>  <tt class="py-line">                <tt class="py-name">args</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-string">"-dAlignToPixels=0"</tt><tt class="py-op">)</tt> </tt>
<a name="L222"></a><tt class="py-lineno"> 222</tt>  <tt class="py-line">         </tt>
<a name="L223"></a><tt class="py-lineno"> 223</tt>  <tt class="py-line">        <tt class="py-name">args</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-string">"-"</tt><tt class="py-op">)</tt>  <tt class="py-comment"># Read from stdin. Must be last argument.</tt> </tt>
<a name="L224"></a><tt class="py-lineno"> 224</tt>  <tt class="py-line">         </tt>
<a name="L225"></a><tt class="py-lineno"> 225</tt>  <tt class="py-line">        <tt class="py-name">error_msg</tt> <tt class="py-op">=</tt> <tt class="py-string">"Unrecoverable error : Ghostscript conversion failed "</tt> \ </tt>
<a name="L226"></a><tt class="py-lineno"> 226</tt>  <tt class="py-line">                    <tt class="py-string">"(Invalid postscript?). %s"</tt> <tt class="py-op">%</tt> <tt class="py-string">" "</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-name">args</tt><tt class="py-op">)</tt>  </tt>
<a name="L227"></a><tt class="py-lineno"> 227</tt>  <tt class="py-line"> </tt>
<a name="L228"></a><tt class="py-lineno"> 228</tt>  <tt class="py-line">        <tt class="py-name">source</tt> <tt class="py-op">=</tt> <tt class="py-name">fin</tt><tt class="py-op">.</tt><tt class="py-name">read</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L229"></a><tt class="py-lineno"> 229</tt>  <tt class="py-line">        <tt class="py-keyword">try</tt> <tt class="py-op">:</tt> </tt>
<a name="L230"></a><tt class="py-lineno"> 230</tt>  <tt class="py-line">            <tt class="py-name">p</tt> <tt class="py-op">=</tt> <tt class="py-name">Popen</tt><tt class="py-op">(</tt><tt class="py-name">args</tt><tt class="py-op">,</tt> <tt class="py-name">stdin</tt><tt class="py-op">=</tt><tt class="py-name">PIPE</tt><tt class="py-op">,</tt> <tt class="py-name">stdout</tt> <tt class="py-op">=</tt> <tt class="py-name">PIPE</tt><tt class="py-op">,</tt> <tt class="py-name">stderr</tt><tt class="py-op">=</tt> <tt class="py-name">PIPE</tt><tt class="py-op">)</tt>  </tt>
<a name="L231"></a><tt class="py-lineno"> 231</tt>  <tt class="py-line">            <tt class="py-op">(</tt><tt class="py-name">out</tt><tt class="py-op">,</tt><tt class="py-name">err</tt><tt class="py-op">)</tt> <tt class="py-op">=</tt> <tt class="py-name">p</tt><tt class="py-op">.</tt><tt class="py-name">communicate</tt><tt class="py-op">(</tt><tt class="py-name">source</tt><tt class="py-op">)</tt>  </tt>
<a name="L232"></a><tt class="py-lineno"> 232</tt>  <tt class="py-line">        <tt class="py-keyword">except</tt> <tt class="py-name">OSError</tt> <tt class="py-op">:</tt> </tt>
<a name="L233"></a><tt class="py-lineno"> 233</tt>  <tt class="py-line">            <tt class="py-keyword">raise</tt> <tt class="py-name">RuntimeError</tt><tt class="py-op">(</tt><tt class="py-name">error_msg</tt><tt class="py-op">)</tt> </tt>
<a name="L234"></a><tt class="py-lineno"> 234</tt>  <tt class="py-line">     </tt>
<a name="L235"></a><tt class="py-lineno"> 235</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">p</tt><tt class="py-op">.</tt><tt class="py-name">returncode</tt> <tt class="py-op">!=</tt> <tt class="py-number">0</tt> <tt class="py-op">:</tt>  </tt>
<a name="L236"></a><tt class="py-lineno"> 236</tt>  <tt class="py-line">            <tt class="py-name">error_msg</tt> <tt class="py-op">+=</tt> <tt class="py-string">'\nReturn code: %i\n'</tt> <tt class="py-op">%</tt> <tt class="py-name">p</tt><tt class="py-op">.</tt><tt class="py-name">returncode</tt>  </tt>
<a name="L237"></a><tt class="py-lineno"> 237</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">err</tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</tt> <tt class="py-op">:</tt> <tt class="py-name">error_msg</tt> <tt class="py-op">+=</tt> <tt class="py-name">err</tt> </tt>
<a name="L238"></a><tt class="py-lineno"> 238</tt>  <tt class="py-line">            <tt class="py-keyword">raise</tt> <tt class="py-name">RuntimeError</tt><tt class="py-op">(</tt><tt class="py-name">error_msg</tt><tt class="py-op">)</tt> </tt>
<a name="L239"></a><tt class="py-lineno"> 239</tt>  <tt class="py-line">         </tt>
<a name="L240"></a><tt class="py-lineno"> 240</tt>  <tt class="py-line">        <tt class="py-keyword">print</tt> <tt class="py-op">&gt;&gt;</tt><tt class="py-name">fout</tt><tt class="py-op">,</tt> <tt class="py-name">out</tt> </tt>
</div></div><a name="L241"></a><tt class="py-lineno"> 241</tt>  <tt class="py-line"><tt class="py-comment"># end class Ghostscript</tt> </tt>
<a name="L242"></a><tt class="py-lineno"> 242</tt>  <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L243"></a><tt class="py-lineno"> 243</tt>  <tt class="py-line"> </tt>
<a name="L244"></a><tt class="py-lineno"> 244</tt>  <tt class="py-line"><tt id="link-16" class="py-name" targets="Variable weblogolib.aa_composition=weblogolib-module.html#aa_composition"><a title="weblogolib.aa_composition" class="py-name" href="#" onclick="return doclink('link-16', 'aa_composition', 'link-16');">aa_composition</a></tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt> <tt class="py-name">amino_acid_composition</tt><tt class="py-op">[</tt><tt class="py-name">_k</tt><tt class="py-op">]</tt> <tt class="py-keyword">for</tt> <tt class="py-name">_k</tt> <tt class="py-keyword">in</tt> </tt>
<a name="L245"></a><tt class="py-lineno"> 245</tt>  <tt class="py-line">                    <tt class="py-name">unambiguous_protein_alphabet</tt><tt class="py-op">]</tt> </tt>
<a name="L246"></a><tt class="py-lineno"> 246</tt>  <tt class="py-line"> </tt>
<a name="L247"></a><tt class="py-lineno"> 247</tt>  <tt class="py-line"> </tt>
<a name="L248"></a><tt class="py-lineno"> 248</tt>  <tt class="py-line"> </tt>
<a name="L249"></a><tt class="py-lineno"> 249</tt>  <tt class="py-line"><tt class="py-comment"># ------  DATA ------</tt> </tt>
<a name="L250"></a><tt class="py-lineno"> 250</tt>  <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L251"></a><tt class="py-lineno"> 251</tt>  <tt class="py-line"><tt id="link-17" class="py-name" targets="Variable weblogolib.classic=weblogolib-module.html#classic"><a title="weblogolib.classic" class="py-name" href="#" onclick="return doclink('link-17', 'classic', 'link-17');">classic</a></tt> <tt class="py-op">=</tt> <tt id="link-18" class="py-name" targets="Class weblogolib.colorscheme.ColorScheme=weblogolib.colorscheme.ColorScheme-class.html"><a title="weblogolib.colorscheme.ColorScheme" class="py-name" href="#" onclick="return doclink('link-18', 'ColorScheme', 'link-18');">ColorScheme</a></tt><tt class="py-op">(</tt><tt class="py-op">[</tt> </tt>
<a name="L252"></a><tt class="py-lineno"> 252</tt>  <tt class="py-line">    <tt id="link-19" class="py-name" targets="Class weblogolib.colorscheme.ColorGroup=weblogolib.colorscheme.ColorGroup-class.html"><a title="weblogolib.colorscheme.ColorGroup" class="py-name" href="#" onclick="return doclink('link-19', 'ColorGroup', 'link-19');">ColorGroup</a></tt><tt class="py-op">(</tt><tt class="py-string">"G"</tt><tt class="py-op">,</tt>  <tt class="py-string">"orange"</tt> <tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L253"></a><tt class="py-lineno"> 253</tt>  <tt class="py-line">    <tt id="link-20" class="py-name"><a title="weblogolib.colorscheme.ColorGroup" class="py-name" href="#" onclick="return doclink('link-20', 'ColorGroup', 'link-19');">ColorGroup</a></tt><tt class="py-op">(</tt><tt class="py-string">"TU"</tt><tt class="py-op">,</tt> <tt class="py-string">"red"</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L254"></a><tt class="py-lineno"> 254</tt>  <tt class="py-line">    <tt id="link-21" class="py-name"><a title="weblogolib.colorscheme.ColorGroup" class="py-name" href="#" onclick="return doclink('link-21', 'ColorGroup', 'link-19');">ColorGroup</a></tt><tt class="py-op">(</tt><tt class="py-string">"C"</tt><tt class="py-op">,</tt>  <tt class="py-string">"blue"</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L255"></a><tt class="py-lineno"> 255</tt>  <tt class="py-line">    <tt id="link-22" class="py-name"><a title="weblogolib.colorscheme.ColorGroup" class="py-name" href="#" onclick="return doclink('link-22', 'ColorGroup', 'link-19');">ColorGroup</a></tt><tt class="py-op">(</tt><tt class="py-string">"A"</tt><tt class="py-op">,</tt>  <tt class="py-string">"green"</tt><tt class="py-op">)</tt> </tt>
<a name="L256"></a><tt class="py-lineno"> 256</tt>  <tt class="py-line">    <tt class="py-op">]</tt> <tt class="py-op">)</tt> </tt>
<a name="L257"></a><tt class="py-lineno"> 257</tt>  <tt class="py-line">     </tt>
<a name="L258"></a><tt class="py-lineno"> 258</tt>  <tt class="py-line"><tt id="link-23" class="py-name" targets="Variable weblogolib.std_color_schemes=weblogolib-module.html#std_color_schemes"><a title="weblogolib.std_color_schemes" class="py-name" href="#" onclick="return doclink('link-23', 'std_color_schemes', 'link-23');">std_color_schemes</a></tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-string">"auto"</tt><tt class="py-op">:</tt>            <tt class="py-name">None</tt><tt class="py-op">,</tt>   <tt class="py-comment"># Depends on sequence type</tt> </tt>
<a name="L259"></a><tt class="py-lineno"> 259</tt>  <tt class="py-line">                     <tt class="py-string">"monochrome"</tt><tt class="py-op">:</tt>      <tt id="link-24" class="py-name" targets="Variable weblogolib.colorscheme.monochrome=weblogolib.colorscheme-module.html#monochrome"><a title="weblogolib.colorscheme.monochrome" class="py-name" href="#" onclick="return doclink('link-24', 'monochrome', 'link-24');">monochrome</a></tt><tt class="py-op">,</tt> </tt>
<a name="L260"></a><tt class="py-lineno"> 260</tt>  <tt class="py-line">                     <tt class="py-string">"base pairing"</tt><tt class="py-op">:</tt>    <tt id="link-25" class="py-name" targets="Variable weblogolib.colorscheme.base_pairing=weblogolib.colorscheme-module.html#base_pairing"><a title="weblogolib.colorscheme.base_pairing" class="py-name" href="#" onclick="return doclink('link-25', 'base_pairing', 'link-25');">base_pairing</a></tt><tt class="py-op">,</tt> </tt>
<a name="L261"></a><tt class="py-lineno"> 261</tt>  <tt class="py-line">                     <tt class="py-string">"classic"</tt><tt class="py-op">:</tt>         <tt id="link-26" class="py-name"><a title="weblogolib.classic" class="py-name" href="#" onclick="return doclink('link-26', 'classic', 'link-17');">classic</a></tt><tt class="py-op">,</tt> </tt>
<a name="L262"></a><tt class="py-lineno"> 262</tt>  <tt class="py-line">                     <tt class="py-string">"hydrophobicity"</tt> <tt class="py-op">:</tt> <tt id="link-27" class="py-name" targets="Variable weblogolib.colorscheme.hydrophobicity=weblogolib.colorscheme-module.html#hydrophobicity"><a title="weblogolib.colorscheme.hydrophobicity" class="py-name" href="#" onclick="return doclink('link-27', 'hydrophobicity', 'link-27');">hydrophobicity</a></tt><tt class="py-op">,</tt>   </tt>
<a name="L263"></a><tt class="py-lineno"> 263</tt>  <tt class="py-line">                     <tt class="py-string">"chemistry"</tt> <tt class="py-op">:</tt>      <tt id="link-28" class="py-name" targets="Variable weblogolib.colorscheme.chemistry=weblogolib.colorscheme-module.html#chemistry"><a title="weblogolib.colorscheme.chemistry" class="py-name" href="#" onclick="return doclink('link-28', 'chemistry', 'link-28');">chemistry</a></tt><tt class="py-op">,</tt> </tt>
<a name="L264"></a><tt class="py-lineno"> 264</tt>  <tt class="py-line">                     <tt class="py-string">"charge"</tt> <tt class="py-op">:</tt>         <tt id="link-29" class="py-name" targets="Variable weblogolib.colorscheme.charge=weblogolib.colorscheme-module.html#charge"><a title="weblogolib.colorscheme.charge" class="py-name" href="#" onclick="return doclink('link-29', 'charge', 'link-29');">charge</a></tt><tt class="py-op">,</tt> </tt>
<a name="L265"></a><tt class="py-lineno"> 265</tt>  <tt class="py-line">                     <tt class="py-op">}</tt><tt class="py-comment">#</tt> </tt>
<a name="L266"></a><tt class="py-lineno"> 266</tt>  <tt class="py-line"> </tt>
<a name="L267"></a><tt class="py-lineno"> 267</tt>  <tt class="py-line"><tt id="link-30" class="py-name" targets="Variable weblogolib.default_color_schemes=weblogolib-module.html#default_color_schemes"><a title="weblogolib.default_color_schemes" class="py-name" href="#" onclick="return doclink('link-30', 'default_color_schemes', 'link-30');">default_color_schemes</a></tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt> </tt>
<a name="L268"></a><tt class="py-lineno"> 268</tt>  <tt class="py-line">    <tt class="py-name">unambiguous_protein_alphabet</tt><tt class="py-op">:</tt> <tt id="link-31" class="py-name"><a title="weblogolib.colorscheme.hydrophobicity" class="py-name" href="#" onclick="return doclink('link-31', 'hydrophobicity', 'link-27');">hydrophobicity</a></tt><tt class="py-op">,</tt>  </tt>
<a name="L269"></a><tt class="py-lineno"> 269</tt>  <tt class="py-line">    <tt class="py-name">unambiguous_rna_alphabet</tt><tt class="py-op">:</tt> <tt id="link-32" class="py-name"><a title="weblogolib.colorscheme.base_pairing" class="py-name" href="#" onclick="return doclink('link-32', 'base_pairing', 'link-25');">base_pairing</a></tt><tt class="py-op">,</tt> </tt>
<a name="L270"></a><tt class="py-lineno"> 270</tt>  <tt class="py-line">    <tt class="py-name">unambiguous_dna_alphabet</tt><tt class="py-op">:</tt> <tt id="link-33" class="py-name"><a title="weblogolib.colorscheme.base_pairing" class="py-name" href="#" onclick="return doclink('link-33', 'base_pairing', 'link-25');">base_pairing</a></tt>  </tt>
<a name="L271"></a><tt class="py-lineno"> 271</tt>  <tt class="py-line"><tt class="py-op">}</tt> </tt>
<a name="L272"></a><tt class="py-lineno"> 272</tt>  <tt class="py-line"> </tt>
<a name="L273"></a><tt class="py-lineno"> 273</tt>  <tt class="py-line"><tt id="link-34" class="py-name" targets="Variable weblogolib.std_units=weblogolib-module.html#std_units"><a title="weblogolib.std_units" class="py-name" href="#" onclick="return doclink('link-34', 'std_units', 'link-34');">std_units</a></tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt> </tt>
<a name="L274"></a><tt class="py-lineno"> 274</tt>  <tt class="py-line">    <tt class="py-string">"bits"</tt>    <tt class="py-op">:</tt> <tt class="py-number">1.</tt><tt class="py-op">/</tt><tt class="py-name">log</tt><tt class="py-op">(</tt><tt class="py-number">2</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L275"></a><tt class="py-lineno"> 275</tt>  <tt class="py-line">    <tt class="py-string">"nats"</tt>    <tt class="py-op">:</tt> <tt class="py-number">1.</tt><tt class="py-op">,</tt> </tt>
<a name="L276"></a><tt class="py-lineno"> 276</tt>  <tt class="py-line">    <tt class="py-string">"digits"</tt>  <tt class="py-op">:</tt> <tt class="py-number">1.</tt><tt class="py-op">/</tt><tt class="py-name">log</tt><tt class="py-op">(</tt><tt class="py-number">10</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L277"></a><tt class="py-lineno"> 277</tt>  <tt class="py-line">    <tt class="py-string">"kT"</tt>      <tt class="py-op">:</tt> <tt class="py-number">1.</tt><tt class="py-op">,</tt> </tt>
<a name="L278"></a><tt class="py-lineno"> 278</tt>  <tt class="py-line">    <tt class="py-string">"kJ/mol"</tt>  <tt class="py-op">:</tt> <tt class="py-number">8.314472</tt> <tt class="py-op">*</tt><tt class="py-number">298.15</tt> <tt class="py-op">/</tt><tt class="py-number">1000.</tt><tt class="py-op">,</tt> </tt>
<a name="L279"></a><tt class="py-lineno"> 279</tt>  <tt class="py-line">    <tt class="py-string">"kcal/mol"</tt><tt class="py-op">:</tt> <tt class="py-number">1.987</tt> <tt class="py-op">*</tt><tt class="py-number">298.15</tt>  <tt class="py-op">/</tt><tt class="py-number">1000.</tt><tt class="py-op">,</tt> </tt>
<a name="L280"></a><tt class="py-lineno"> 280</tt>  <tt class="py-line">    <tt class="py-string">"probability"</tt> <tt class="py-op">:</tt> <tt class="py-name">None</tt><tt class="py-op">,</tt> </tt>
<a name="L281"></a><tt class="py-lineno"> 281</tt>  <tt class="py-line"><tt class="py-op">}</tt> </tt>
<a name="L282"></a><tt class="py-lineno"> 282</tt>  <tt class="py-line"> </tt>
<a name="L283"></a><tt class="py-lineno"> 283</tt>  <tt class="py-line"><tt class="py-comment"># The base stack width is set equal to 9pt Courier. </tt> </tt>
<a name="L284"></a><tt class="py-lineno"> 284</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># (Courier has a width equal to 3/5 of the point size.)</tt> </tt>
<a name="L285"></a><tt class="py-lineno"> 285</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># Check that can get 80 characters in journal page @small</tt> </tt>
<a name="L286"></a><tt class="py-lineno"> 286</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># 40 characters in a journal column</tt> </tt>
<a name="L287"></a><tt class="py-lineno"> 287</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt id="link-35" class="py-name" targets="Variable weblogolib.std_sizes=weblogolib-module.html#std_sizes"><a title="weblogolib.std_sizes" class="py-name" href="#" onclick="return doclink('link-35', 'std_sizes', 'link-35');">std_sizes</a></tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt> </tt>
<a name="L288"></a><tt class="py-lineno"> 288</tt>  <tt class="py-line">    <tt class="py-string">"small"</tt> <tt class="py-op">:</tt> <tt class="py-number">5.4</tt> <tt class="py-op">,</tt>  </tt>
<a name="L289"></a><tt class="py-lineno"> 289</tt>  <tt class="py-line">    <tt class="py-string">"medium"</tt> <tt class="py-op">:</tt> <tt class="py-number">5.4</tt><tt class="py-op">*</tt><tt class="py-number">2</tt><tt class="py-op">,</tt> </tt>
<a name="L290"></a><tt class="py-lineno"> 290</tt>  <tt class="py-line">    <tt class="py-string">"large"</tt>  <tt class="py-op">:</tt> <tt class="py-number">5.4</tt><tt class="py-op">*</tt><tt class="py-number">3</tt> </tt>
<a name="L291"></a><tt class="py-lineno"> 291</tt>  <tt class="py-line"><tt class="py-op">}</tt> </tt>
<a name="L292"></a><tt class="py-lineno"> 292</tt>  <tt class="py-line">             </tt>
<a name="L293"></a><tt class="py-lineno"> 293</tt>  <tt class="py-line"><tt id="link-36" class="py-name" targets="Variable weblogolib.std_alphabets=weblogolib-module.html#std_alphabets"><a title="weblogolib.std_alphabets" class="py-name" href="#" onclick="return doclink('link-36', 'std_alphabets', 'link-36');">std_alphabets</a></tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt> </tt>
<a name="L294"></a><tt class="py-lineno"> 294</tt>  <tt class="py-line">    <tt class="py-string">'protein'</tt><tt class="py-op">:</tt> <tt class="py-name">unambiguous_protein_alphabet</tt><tt class="py-op">,</tt>  </tt>
<a name="L295"></a><tt class="py-lineno"> 295</tt>  <tt class="py-line">    <tt class="py-string">'rna'</tt><tt class="py-op">:</tt> <tt class="py-name">unambiguous_rna_alphabet</tt><tt class="py-op">,</tt> </tt>
<a name="L296"></a><tt class="py-lineno"> 296</tt>  <tt class="py-line">    <tt class="py-string">'dna'</tt><tt class="py-op">:</tt> <tt class="py-name">unambiguous_dna_alphabet</tt><tt class="py-op">}</tt> </tt>
<a name="L297"></a><tt class="py-lineno"> 297</tt>  <tt class="py-line"> </tt>
<a name="L298"></a><tt class="py-lineno"> 298</tt>  <tt class="py-line"><tt id="link-37" class="py-name" targets="Variable weblogolib.std_percentCG=weblogolib-module.html#std_percentCG"><a title="weblogolib.std_percentCG" class="py-name" href="#" onclick="return doclink('link-37', 'std_percentCG', 'link-37');">std_percentCG</a></tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt> </tt>
<a name="L299"></a><tt class="py-lineno"> 299</tt>  <tt class="py-line">    <tt class="py-string">'H. sapiens'</tt>    <tt class="py-op">:</tt> <tt class="py-number">40.</tt><tt class="py-op">,</tt> </tt>
<a name="L300"></a><tt class="py-lineno"> 300</tt>  <tt class="py-line">    <tt class="py-string">'E. coli'</tt>       <tt class="py-op">:</tt> <tt class="py-number">50.5</tt><tt class="py-op">,</tt> </tt>
<a name="L301"></a><tt class="py-lineno"> 301</tt>  <tt class="py-line">    <tt class="py-string">'S. cerevisiae'</tt> <tt class="py-op">:</tt> <tt class="py-number">38.</tt><tt class="py-op">,</tt> </tt>
<a name="L302"></a><tt class="py-lineno"> 302</tt>  <tt class="py-line">    <tt class="py-string">'C. elegans'</tt>    <tt class="py-op">:</tt> <tt class="py-number">36.</tt><tt class="py-op">,</tt> </tt>
<a name="L303"></a><tt class="py-lineno"> 303</tt>  <tt class="py-line">    <tt class="py-string">'D. melanogaster'</tt><tt class="py-op">:</tt> <tt class="py-number">43.</tt><tt class="py-op">,</tt> </tt>
<a name="L304"></a><tt class="py-lineno"> 304</tt>  <tt class="py-line">    <tt class="py-string">'M. musculus'</tt>   <tt class="py-op">:</tt>  <tt class="py-number">42.</tt><tt class="py-op">,</tt> </tt>
<a name="L305"></a><tt class="py-lineno"> 305</tt>  <tt class="py-line">    <tt class="py-string">'T. thermophilus'</tt> <tt class="py-op">:</tt> <tt class="py-number">69.4</tt><tt class="py-op">,</tt> </tt>
<a name="L306"></a><tt class="py-lineno"> 306</tt>  <tt class="py-line"><tt class="py-op">}</tt> </tt>
<a name="LogoOptions"></a><div id="LogoOptions-def"><a name="L307"></a><tt class="py-lineno"> 307</tt>  <tt class="py-line"> </tt>
<a name="L308"></a><tt class="py-lineno"> 308</tt>  <tt class="py-line"><tt class="py-comment"># Thermus thermophilus: Henne A, Bruggemann H, Raasch C, Wiezer A, Hartsch T,</tt> </tt>
<a name="L309"></a><tt class="py-lineno"> 309</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># Liesegang H, Johann A, Lienard T, Gohl O, Martinez-Arias R, Jacobi C, </tt> </tt>
<a name="L310"></a><tt class="py-lineno"> 310</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># Starkuviene V, Schlenczeck S, Dencker S, Huber R, Klenk HP, Kramer W, </tt> </tt>
<a name="L311"></a><tt class="py-lineno"> 311</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># Merkl R, Gottschalk G, Fritz HJ: The genome sequence of the extreme </tt> </tt>
<a name="L312"></a><tt class="py-lineno"> 312</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># thermophile Thermus thermophilus.</tt> </tt>
<a name="L313"></a><tt class="py-lineno"> 313</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># Nat Biotechnol 2004, 22:547-53</tt> </tt>
<a name="L314"></a><tt class="py-lineno"> 314</tt>  <tt class="py-line"><tt class="py-comment"></tt>             </tt>
<a name="L315"></a><tt class="py-lineno"> 315</tt>  <tt class="py-line"> </tt>
<a name="L316"></a><tt class="py-lineno"> 316</tt>  <tt class="py-line">   </tt>
<a name="L317"></a><tt class="py-lineno"> 317</tt> <a class="py-toggle" href="#" id="LogoOptions-toggle" onclick="return toggle('LogoOptions');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="weblogolib.LogoOptions-class.html">LogoOptions</a><tt class="py-op">(</tt><tt class="py-base-class">object</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
</div><div id="LogoOptions-collapsed" style="display:none;" pad="++++" indent="++++"></div><div id="LogoOptions-expanded"><a name="L318"></a><tt class="py-lineno"> 318</tt>  <tt class="py-line">    <tt class="py-docstring">""" A container for all logo formatting options. Not all of these</tt> </tt>
<a name="L319"></a><tt class="py-lineno"> 319</tt>  <tt class="py-line"><tt class="py-docstring">    are directly accessible through the CLI or web interfaces. </tt> </tt>
<a name="L320"></a><tt class="py-lineno"> 320</tt>  <tt class="py-line"><tt class="py-docstring">    </tt> </tt>
<a name="L321"></a><tt class="py-lineno"> 321</tt>  <tt class="py-line"><tt class="py-docstring">    To display LogoOption defaults:</tt> </tt>
<a name="L322"></a><tt class="py-lineno"> 322</tt>  <tt class="py-line"><tt class="py-docstring">    &gt;&gt;&gt; from weblogolib import *</tt> </tt>
<a name="L323"></a><tt class="py-lineno"> 323</tt>  <tt class="py-line"><tt class="py-docstring">    &gt;&gt;&gt; LogoOptions()</tt> </tt>
<a name="L324"></a><tt class="py-lineno"> 324</tt>  <tt class="py-line"><tt class="py-docstring">    </tt> </tt>
<a name="L325"></a><tt class="py-lineno"> 325</tt>  <tt class="py-line"><tt class="py-docstring">    All physical lengths are measured in points. (72 points per inch, 28.3 points per cm)</tt> </tt>
<a name="L326"></a><tt class="py-lineno"> 326</tt>  <tt class="py-line"><tt class="py-docstring">      </tt> </tt>
<a name="L327"></a><tt class="py-lineno"> 327</tt>  <tt class="py-line"><tt class="py-docstring">    String attributes:</tt> </tt>
<a name="L328"></a><tt class="py-lineno"> 328</tt>  <tt class="py-line"><tt class="py-docstring">        o creator_text      -- Embedded as comment in figures.</tt> </tt>
<a name="L329"></a><tt class="py-lineno"> 329</tt>  <tt class="py-line"><tt class="py-docstring">        o logo_title             </tt> </tt>
<a name="L330"></a><tt class="py-lineno"> 330</tt>  <tt class="py-line"><tt class="py-docstring">        o logo_label</tt> </tt>
<a name="L331"></a><tt class="py-lineno"> 331</tt>  <tt class="py-line"><tt class="py-docstring">        o unit_name         -- See std_units for options. (Default 'bits') </tt> </tt>
<a name="L332"></a><tt class="py-lineno"> 332</tt>  <tt class="py-line"><tt class="py-docstring">        o yaxis_label       -- Defaults to unit_name      </tt> </tt>
<a name="L333"></a><tt class="py-lineno"> 333</tt>  <tt class="py-line"><tt class="py-docstring">        o xaxis_label</tt> </tt>
<a name="L334"></a><tt class="py-lineno"> 334</tt>  <tt class="py-line"><tt class="py-docstring">        o fineprint         -- Defaults to WebLogo name and version</tt> </tt>
<a name="L335"></a><tt class="py-lineno"> 335</tt>  <tt class="py-line"><tt class="py-docstring">        </tt> </tt>
<a name="L336"></a><tt class="py-lineno"> 336</tt>  <tt class="py-line"><tt class="py-docstring">    Boolean attributes:</tt> </tt>
<a name="L337"></a><tt class="py-lineno"> 337</tt>  <tt class="py-line"><tt class="py-docstring">        o show_yaxis </tt> </tt>
<a name="L338"></a><tt class="py-lineno"> 338</tt>  <tt class="py-line"><tt class="py-docstring">        o show_xaxis         </tt> </tt>
<a name="L339"></a><tt class="py-lineno"> 339</tt>  <tt class="py-line"><tt class="py-docstring">        o show_ends </tt> </tt>
<a name="L340"></a><tt class="py-lineno"> 340</tt>  <tt class="py-line"><tt class="py-docstring">        o show_fineprint        </tt> </tt>
<a name="L341"></a><tt class="py-lineno"> 341</tt>  <tt class="py-line"><tt class="py-docstring">        o show_errorbars    -- Draw errorbars (default: False)</tt> </tt>
<a name="L342"></a><tt class="py-lineno"> 342</tt>  <tt class="py-line"><tt class="py-docstring">        o show_boxes        -- Draw boxes around stack characters (default: True)</tt> </tt>
<a name="L343"></a><tt class="py-lineno"> 343</tt>  <tt class="py-line"><tt class="py-docstring">        o debug             -- Draw extra graphics debugging information. </tt> </tt>
<a name="L344"></a><tt class="py-lineno"> 344</tt>  <tt class="py-line"><tt class="py-docstring">        o rotate_numbers    -- Draw xaxis numbers with vertical orientation? </tt> </tt>
<a name="L345"></a><tt class="py-lineno"> 345</tt>  <tt class="py-line"><tt class="py-docstring">        o scale_width       -- boolean, scale width of characters proportional to ungaps</tt> </tt>
<a name="L346"></a><tt class="py-lineno"> 346</tt>  <tt class="py-line"><tt class="py-docstring">        o pad_right         -- Make a single line logo the same width as multiline logos (default: False)                           </tt> </tt>
<a name="L347"></a><tt class="py-lineno"> 347</tt>  <tt class="py-line"><tt class="py-docstring">                                </tt> </tt>
<a name="L348"></a><tt class="py-lineno"> 348</tt>  <tt class="py-line"><tt class="py-docstring">    Other attributes:</tt> </tt>
<a name="L349"></a><tt class="py-lineno"> 349</tt>  <tt class="py-line"><tt class="py-docstring">        o stacks_per_line</tt> </tt>
<a name="L350"></a><tt class="py-lineno"> 350</tt>  <tt class="py-line"><tt class="py-docstring">        </tt> </tt>
<a name="L351"></a><tt class="py-lineno"> 351</tt>  <tt class="py-line"><tt class="py-docstring">        o yaxis_tic_interval </tt> </tt>
<a name="L352"></a><tt class="py-lineno"> 352</tt>  <tt class="py-line"><tt class="py-docstring">        o yaxis_minor_tic_ratio </tt> </tt>
<a name="L353"></a><tt class="py-lineno"> 353</tt>  <tt class="py-line"><tt class="py-docstring">        o yaxis_scale</tt> </tt>
<a name="L354"></a><tt class="py-lineno"> 354</tt>  <tt class="py-line"><tt class="py-docstring">        o xaxis_tic_interval </tt> </tt>
<a name="L355"></a><tt class="py-lineno"> 355</tt>  <tt class="py-line"><tt class="py-docstring">        o number_interval</tt> </tt>
<a name="L356"></a><tt class="py-lineno"> 356</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L357"></a><tt class="py-lineno"> 357</tt>  <tt class="py-line"><tt class="py-docstring">        o shrink_fraction       -- Proportional shrinkage of characters if show_boxes is true.</tt> </tt>
<a name="L358"></a><tt class="py-lineno"> 358</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L359"></a><tt class="py-lineno"> 359</tt>  <tt class="py-line"><tt class="py-docstring">        o errorbar_fraction </tt> </tt>
<a name="L360"></a><tt class="py-lineno"> 360</tt>  <tt class="py-line"><tt class="py-docstring">        o errorbar_width_fraction </tt> </tt>
<a name="L361"></a><tt class="py-lineno"> 361</tt>  <tt class="py-line"><tt class="py-docstring">        o errorbar_gray </tt> </tt>
<a name="L362"></a><tt class="py-lineno"> 362</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L363"></a><tt class="py-lineno"> 363</tt>  <tt class="py-line"><tt class="py-docstring">        o resolution             -- Dots per inch (default: 96). Used for bitmapped output formats</tt> </tt>
<a name="L364"></a><tt class="py-lineno"> 364</tt>  <tt class="py-line"><tt class="py-docstring">        </tt> </tt>
<a name="L365"></a><tt class="py-lineno"> 365</tt>  <tt class="py-line"><tt class="py-docstring">        o default_color </tt> </tt>
<a name="L366"></a><tt class="py-lineno"> 366</tt>  <tt class="py-line"><tt class="py-docstring">        o color_scheme </tt> </tt>
<a name="L367"></a><tt class="py-lineno"> 367</tt>  <tt class="py-line"><tt class="py-docstring">        </tt> </tt>
<a name="L368"></a><tt class="py-lineno"> 368</tt>  <tt class="py-line"><tt class="py-docstring">        o stack_width           --</tt> </tt>
<a name="L369"></a><tt class="py-lineno"> 369</tt>  <tt class="py-line"><tt class="py-docstring">        o stack_aspect_ratio    -- Ratio of stack height to width (default: 5)</tt> </tt>
<a name="L370"></a><tt class="py-lineno"> 370</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L371"></a><tt class="py-lineno"> 371</tt>  <tt class="py-line"><tt class="py-docstring">        o logo_margin           -- Default: 2 pts</tt> </tt>
<a name="L372"></a><tt class="py-lineno"> 372</tt>  <tt class="py-line"><tt class="py-docstring">        o stroke_width          -- Default: 0.5 pts</tt> </tt>
<a name="L373"></a><tt class="py-lineno"> 373</tt>  <tt class="py-line"><tt class="py-docstring">        o tic_length            -- Default: 5 pts</tt> </tt>
<a name="L374"></a><tt class="py-lineno"> 374</tt>  <tt class="py-line"><tt class="py-docstring">        o stack_margin          -- Default: 0.5 pts</tt> </tt>
<a name="L375"></a><tt class="py-lineno"> 375</tt>  <tt class="py-line"><tt class="py-docstring">        </tt> </tt>
<a name="L376"></a><tt class="py-lineno"> 376</tt>  <tt class="py-line"><tt class="py-docstring">        o small_fontsize        -- Small text font size in points</tt> </tt>
<a name="L377"></a><tt class="py-lineno"> 377</tt>  <tt class="py-line"><tt class="py-docstring">        o fontsize              -- Regular text font size in points</tt> </tt>
<a name="L378"></a><tt class="py-lineno"> 378</tt>  <tt class="py-line"><tt class="py-docstring">        o title_fontsize        -- Title text font size in points</tt> </tt>
<a name="L379"></a><tt class="py-lineno"> 379</tt>  <tt class="py-line"><tt class="py-docstring">        o number_fontsize       -- Font size for axis-numbers, in points.</tt> </tt>
<a name="L380"></a><tt class="py-lineno"> 380</tt>  <tt class="py-line"><tt class="py-docstring">        </tt> </tt>
<a name="L381"></a><tt class="py-lineno"> 381</tt>  <tt class="py-line"><tt class="py-docstring">        o text_font</tt> </tt>
<a name="L382"></a><tt class="py-lineno"> 382</tt>  <tt class="py-line"><tt class="py-docstring">        o logo_font</tt> </tt>
<a name="L383"></a><tt class="py-lineno"> 383</tt>  <tt class="py-line"><tt class="py-docstring">        o title_font</tt> </tt>
<a name="L384"></a><tt class="py-lineno"> 384</tt>  <tt class="py-line"><tt class="py-docstring">        </tt> </tt>
<a name="L385"></a><tt class="py-lineno"> 385</tt>  <tt class="py-line"><tt class="py-docstring">        o first_index</tt> </tt>
<a name="L386"></a><tt class="py-lineno"> 386</tt>  <tt class="py-line"><tt class="py-docstring">        o logo_start</tt> </tt>
<a name="L387"></a><tt class="py-lineno"> 387</tt>  <tt class="py-line"><tt class="py-docstring">        o logo_end</tt> </tt>
<a name="L388"></a><tt class="py-lineno"> 388</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L389"></a><tt class="py-lineno"> 389</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt>        </tt>
<a name="L390"></a><tt class="py-lineno"> 390</tt>  <tt class="py-line"> </tt>
<a name="LogoOptions.__init__"></a><div id="LogoOptions.__init__-def"><a name="L391"></a><tt class="py-lineno"> 391</tt> <a class="py-toggle" href="#" id="LogoOptions.__init__-toggle" onclick="return toggle('LogoOptions.__init__');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="weblogolib.LogoOptions-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-op">**</tt><tt class="py-param">kwargs</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
</div><div id="LogoOptions.__init__-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="LogoOptions.__init__-expanded"><a name="L392"></a><tt class="py-lineno"> 392</tt>  <tt class="py-line">        <tt class="py-docstring">""" Create a new LogoOptions instance.</tt> </tt>
<a name="L393"></a><tt class="py-lineno"> 393</tt>  <tt class="py-line"><tt class="py-docstring">        </tt> </tt>
<a name="L394"></a><tt class="py-lineno"> 394</tt>  <tt class="py-line"><tt class="py-docstring">        &gt;&gt;&gt; L = LogoOptions(logo_title = "Some Title String")</tt> </tt>
<a name="L395"></a><tt class="py-lineno"> 395</tt>  <tt class="py-line"><tt class="py-docstring">        &gt;&gt;&gt; L.show_yaxis = False</tt> </tt>
<a name="L396"></a><tt class="py-lineno"> 396</tt>  <tt class="py-line"><tt class="py-docstring">        &gt;&gt;&gt; repr(L)</tt> </tt>
<a name="L397"></a><tt class="py-lineno"> 397</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L398"></a><tt class="py-lineno"> 398</tt>  <tt class="py-line"> </tt>
<a name="L399"></a><tt class="py-lineno"> 399</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">alphabet</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L400"></a><tt class="py-lineno"> 400</tt>  <tt class="py-line"> </tt>
<a name="L401"></a><tt class="py-lineno"> 401</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">creator_text</tt> <tt class="py-op">=</tt> <tt id="link-38" class="py-name"><a title="weblogolib.release_description" class="py-name" href="#" onclick="return doclink('link-38', 'release_description', 'link-8');">release_description</a></tt> </tt>
<a name="L402"></a><tt class="py-lineno"> 402</tt>  <tt class="py-line">         </tt>
<a name="L403"></a><tt class="py-lineno"> 403</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">logo_title</tt> <tt class="py-op">=</tt> <tt class="py-string">""</tt> </tt>
<a name="L404"></a><tt class="py-lineno"> 404</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">logo_label</tt> <tt class="py-op">=</tt> <tt class="py-string">""</tt> </tt>
<a name="L405"></a><tt class="py-lineno"> 405</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">stacks_per_line</tt> <tt class="py-op">=</tt> <tt class="py-number">40</tt> </tt>
<a name="L406"></a><tt class="py-lineno"> 406</tt>  <tt class="py-line">         </tt>
<a name="L407"></a><tt class="py-lineno"> 407</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">unit_name</tt> <tt class="py-op">=</tt> <tt class="py-string">"bits"</tt> </tt>
<a name="L408"></a><tt class="py-lineno"> 408</tt>  <tt class="py-line">      </tt>
<a name="L409"></a><tt class="py-lineno"> 409</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">show_yaxis</tt> <tt class="py-op">=</tt> <tt class="py-name">True</tt> </tt>
<a name="L410"></a><tt class="py-lineno"> 410</tt>  <tt class="py-line">        <tt class="py-comment"># yaxis_lable default depends on other settings. See LogoFormat</tt> </tt>
<a name="L411"></a><tt class="py-lineno"> 411</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">yaxis_label</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L412"></a><tt class="py-lineno"> 412</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">yaxis_tic_interval</tt> <tt class="py-op">=</tt> <tt class="py-number">1.</tt> </tt>
<a name="L413"></a><tt class="py-lineno"> 413</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">yaxis_minor_tic_ratio</tt> <tt class="py-op">=</tt> <tt class="py-number">5</tt> </tt>
<a name="L414"></a><tt class="py-lineno"> 414</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">yaxis_scale</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L415"></a><tt class="py-lineno"> 415</tt>  <tt class="py-line"> </tt>
<a name="L416"></a><tt class="py-lineno"> 416</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">show_xaxis</tt> <tt class="py-op">=</tt> <tt class="py-name">True</tt> </tt>
<a name="L417"></a><tt class="py-lineno"> 417</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">xaxis_label</tt> <tt class="py-op">=</tt> <tt class="py-string">""</tt> </tt>
<a name="L418"></a><tt class="py-lineno"> 418</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">xaxis_tic_interval</tt> <tt class="py-op">=</tt><tt class="py-number">1</tt> </tt>
<a name="L419"></a><tt class="py-lineno"> 419</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">rotate_numbers</tt> <tt class="py-op">=</tt> <tt class="py-name">False</tt> </tt>
<a name="L420"></a><tt class="py-lineno"> 420</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">number_interval</tt> <tt class="py-op">=</tt> <tt class="py-number">5</tt>             </tt>
<a name="L421"></a><tt class="py-lineno"> 421</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">show_ends</tt> <tt class="py-op">=</tt> <tt class="py-name">False</tt> </tt>
<a name="L422"></a><tt class="py-lineno"> 422</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">annotate</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L423"></a><tt class="py-lineno"> 423</tt>  <tt class="py-line">         </tt>
<a name="L424"></a><tt class="py-lineno"> 424</tt>  <tt class="py-line">           </tt>
<a name="L425"></a><tt class="py-lineno"> 425</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">show_fineprint</tt> <tt class="py-op">=</tt> <tt class="py-name">True</tt> </tt>
<a name="L426"></a><tt class="py-lineno"> 426</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">fineprint</tt> <tt class="py-op">=</tt>  <tt class="py-string">"WebLogo "</tt><tt class="py-op">+</tt><tt class="py-name">__version__</tt>  </tt>
<a name="L427"></a><tt class="py-lineno"> 427</tt>  <tt class="py-line">     </tt>
<a name="L428"></a><tt class="py-lineno"> 428</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">show_boxes</tt> <tt class="py-op">=</tt> <tt class="py-name">False</tt> </tt>
<a name="L429"></a><tt class="py-lineno"> 429</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">shrink_fraction</tt> <tt class="py-op">=</tt> <tt class="py-number">0.5</tt> </tt>
<a name="L430"></a><tt class="py-lineno"> 430</tt>  <tt class="py-line">   </tt>
<a name="L431"></a><tt class="py-lineno"> 431</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">show_errorbars</tt> <tt class="py-op">=</tt> <tt class="py-name">True</tt> </tt>
<a name="L432"></a><tt class="py-lineno"> 432</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">errorbar_fraction</tt> <tt class="py-op">=</tt> <tt class="py-number">0.90</tt> </tt>
<a name="L433"></a><tt class="py-lineno"> 433</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">errorbar_width_fraction</tt> <tt class="py-op">=</tt> <tt class="py-number">0.25</tt>       </tt>
<a name="L434"></a><tt class="py-lineno"> 434</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">errorbar_gray</tt> <tt class="py-op">=</tt> <tt class="py-number">0.75</tt> </tt>
<a name="L435"></a><tt class="py-lineno"> 435</tt>  <tt class="py-line">  </tt>
<a name="L436"></a><tt class="py-lineno"> 436</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">resolution</tt>  <tt class="py-op">=</tt> <tt class="py-number">96.</tt>     <tt class="py-comment"># Dots per inch</tt> </tt>
<a name="L437"></a><tt class="py-lineno"> 437</tt>  <tt class="py-line">            </tt>
<a name="L438"></a><tt class="py-lineno"> 438</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">default_color</tt> <tt class="py-op">=</tt> <tt id="link-39" class="py-name" targets="Class weblogolib.color.Color=weblogolib.color.Color-class.html"><a title="weblogolib.color.Color" class="py-name" href="#" onclick="return doclink('link-39', 'Color', 'link-39');">Color</a></tt><tt class="py-op">.</tt><tt id="link-40" class="py-name" targets="Static Method weblogolib.color.Color.by_name()=weblogolib.color.Color-class.html#by_name"><a title="weblogolib.color.Color.by_name" class="py-name" href="#" onclick="return doclink('link-40', 'by_name', 'link-40');">by_name</a></tt><tt class="py-op">(</tt><tt class="py-string">"black"</tt><tt class="py-op">)</tt>     </tt>
<a name="L439"></a><tt class="py-lineno"> 439</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">color_scheme</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L440"></a><tt class="py-lineno"> 440</tt>  <tt class="py-line">        <tt class="py-comment">#self.show_color_key = False # NOT yet implemented</tt> </tt>
<a name="L441"></a><tt class="py-lineno"> 441</tt>  <tt class="py-line"><tt class="py-comment"></tt>         </tt>
<a name="L442"></a><tt class="py-lineno"> 442</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">debug</tt> <tt class="py-op">=</tt> <tt class="py-name">False</tt> </tt>
<a name="L443"></a><tt class="py-lineno"> 443</tt>  <tt class="py-line">         </tt>
<a name="L444"></a><tt class="py-lineno"> 444</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">logo_margin</tt> <tt class="py-op">=</tt> <tt class="py-number">2</tt> </tt>
<a name="L445"></a><tt class="py-lineno"> 445</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">stroke_width</tt> <tt class="py-op">=</tt> <tt class="py-number">0.5</tt> </tt>
<a name="L446"></a><tt class="py-lineno"> 446</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">tic_length</tt> <tt class="py-op">=</tt> <tt class="py-number">5</tt> </tt>
<a name="L447"></a><tt class="py-lineno"> 447</tt>  <tt class="py-line">         </tt>
<a name="L448"></a><tt class="py-lineno"> 448</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">stack_width</tt> <tt class="py-op">=</tt> <tt id="link-41" class="py-name"><a title="weblogolib.std_sizes" class="py-name" href="#" onclick="return doclink('link-41', 'std_sizes', 'link-35');">std_sizes</a></tt><tt class="py-op">[</tt><tt class="py-string">"medium"</tt><tt class="py-op">]</tt>         </tt>
<a name="L449"></a><tt class="py-lineno"> 449</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">stack_aspect_ratio</tt> <tt class="py-op">=</tt> <tt class="py-number">5</tt> </tt>
<a name="L450"></a><tt class="py-lineno"> 450</tt>  <tt class="py-line">         </tt>
<a name="L451"></a><tt class="py-lineno"> 451</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">stack_margin</tt> <tt class="py-op">=</tt> <tt class="py-number">0.5</tt> </tt>
<a name="L452"></a><tt class="py-lineno"> 452</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">pad_right</tt> <tt class="py-op">=</tt> <tt class="py-name">False</tt>   </tt>
<a name="L453"></a><tt class="py-lineno"> 453</tt>  <tt class="py-line"> </tt>
<a name="L454"></a><tt class="py-lineno"> 454</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">small_fontsize</tt> <tt class="py-op">=</tt> <tt class="py-number">6</tt> </tt>
<a name="L455"></a><tt class="py-lineno"> 455</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">fontsize</tt> <tt class="py-op">=</tt> <tt class="py-number">10</tt> </tt>
<a name="L456"></a><tt class="py-lineno"> 456</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">title_fontsize</tt> <tt class="py-op">=</tt> <tt class="py-number">12</tt> </tt>
<a name="L457"></a><tt class="py-lineno"> 457</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">number_fontsize</tt> <tt class="py-op">=</tt> <tt class="py-number">8</tt> </tt>
<a name="L458"></a><tt class="py-lineno"> 458</tt>  <tt class="py-line"> </tt>
<a name="L459"></a><tt class="py-lineno"> 459</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">text_font</tt>    <tt class="py-op">=</tt> <tt class="py-string">"ArialMT"</tt> </tt>
<a name="L460"></a><tt class="py-lineno"> 460</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">logo_font</tt>    <tt class="py-op">=</tt> <tt class="py-string">"Arial-BoldMT"</tt> </tt>
<a name="L461"></a><tt class="py-lineno"> 461</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">title_font</tt>   <tt class="py-op">=</tt> <tt class="py-string">"ArialMT"</tt> </tt>
<a name="L462"></a><tt class="py-lineno"> 462</tt>  <tt class="py-line"> </tt>
<a name="L463"></a><tt class="py-lineno"> 463</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">first_index</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt>         </tt>
<a name="L464"></a><tt class="py-lineno"> 464</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">logo_start</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt>       </tt>
<a name="L465"></a><tt class="py-lineno"> 465</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">logo_end</tt><tt class="py-op">=</tt><tt class="py-name">None</tt>           </tt>
<a name="L466"></a><tt class="py-lineno"> 466</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">scale_width</tt> <tt class="py-op">=</tt> <tt class="py-name">True</tt> </tt>
<a name="L467"></a><tt class="py-lineno"> 467</tt>  <tt class="py-line"> </tt>
<a name="L468"></a><tt class="py-lineno"> 468</tt>  <tt class="py-line">        <tt class="py-keyword">from</tt> <tt class="py-name">corebio</tt><tt class="py-op">.</tt><tt class="py-name">utils</tt> <tt class="py-keyword">import</tt> <tt class="py-name">update</tt> </tt>
<a name="L469"></a><tt class="py-lineno"> 469</tt>  <tt class="py-line">        <tt class="py-name">update</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-op">**</tt><tt class="py-name">kwargs</tt><tt class="py-op">)</tt> </tt>
</div><a name="L470"></a><tt class="py-lineno"> 470</tt>  <tt class="py-line"> </tt>
<a name="LogoOptions.__repr__"></a><div id="LogoOptions.__repr__-def"><a name="L471"></a><tt class="py-lineno"> 471</tt> <a class="py-toggle" href="#" id="LogoOptions.__repr__-toggle" onclick="return toggle('LogoOptions.__repr__');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="weblogolib.LogoOptions-class.html#__repr__">__repr__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
</div><div id="LogoOptions.__repr__-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="LogoOptions.__repr__-expanded"><a name="L472"></a><tt class="py-lineno"> 472</tt>  <tt class="py-line">        <tt class="py-keyword">from</tt> <tt class="py-name">corebio</tt><tt class="py-op">.</tt><tt class="py-name">util</tt> <tt class="py-keyword">import</tt> <tt class="py-name">stdrepr</tt> </tt>
<a name="L473"></a><tt class="py-lineno"> 473</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">stdrepr</tt><tt class="py-op">(</tt> <tt class="py-name">self</tt><tt class="py-op">)</tt>  </tt>
</div><a name="L474"></a><tt class="py-lineno"> 474</tt>  <tt class="py-line"> </tt>
<a name="LogoOptions.__repr__"></a><div id="LogoOptions.__repr__-def"><a name="L475"></a><tt class="py-lineno"> 475</tt> <a class="py-toggle" href="#" id="LogoOptions.__repr__-toggle" onclick="return toggle('LogoOptions.__repr__');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="weblogolib.LogoOptions-class.html#__repr__">__repr__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
</div><div id="LogoOptions.__repr__-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="LogoOptions.__repr__-expanded"><a name="L476"></a><tt class="py-lineno"> 476</tt>  <tt class="py-line">        <tt class="py-name">attributes</tt> <tt class="py-op">=</tt> <tt class="py-name">vars</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">keys</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L477"></a><tt class="py-lineno"> 477</tt>  <tt class="py-line">        <tt class="py-name">attributes</tt><tt class="py-op">.</tt><tt class="py-name">sort</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L478"></a><tt class="py-lineno"> 478</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">stdrepr</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-name">attributes</tt> <tt class="py-op">)</tt> </tt>
</div></div><a name="L479"></a><tt class="py-lineno"> 479</tt>  <tt class="py-line">  </tt>
<a name="LogoFormat"></a><div id="LogoFormat-def"><a name="L480"></a><tt class="py-lineno"> 480</tt>  <tt class="py-line"><tt class="py-comment"># End class LogoOptions</tt> </tt>
<a name="L481"></a><tt class="py-lineno"> 481</tt>  <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L482"></a><tt class="py-lineno"> 482</tt>  <tt class="py-line"> </tt>
<a name="L483"></a><tt class="py-lineno"> 483</tt>  <tt class="py-line">         </tt>
<a name="L484"></a><tt class="py-lineno"> 484</tt>  <tt class="py-line"> </tt>
<a name="L485"></a><tt class="py-lineno"> 485</tt> <a class="py-toggle" href="#" id="LogoFormat-toggle" onclick="return toggle('LogoFormat');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="weblogolib.LogoFormat-class.html">LogoFormat</a><tt class="py-op">(</tt><tt class="py-base-class">LogoOptions</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt>      </tt>
</div><a name="L486"></a><tt class="py-lineno"> 486</tt>  <tt class="py-line">    <tt class="py-docstring">""" Specifies the format of the logo. Requires LogoData and LogoOptions </tt> </tt>
<a name="L487"></a><tt class="py-lineno"> 487</tt>  <tt class="py-line"><tt class="py-docstring">    objects.</tt> </tt>
<a name="L488"></a><tt class="py-lineno"> 488</tt>  <tt class="py-line"><tt class="py-docstring">    </tt> </tt>
<a name="L489"></a><tt class="py-lineno"> 489</tt>  <tt class="py-line"><tt class="py-docstring">    &gt;&gt;&gt; data = LogoData.from_seqs(seqs )</tt> </tt>
<a name="L490"></a><tt class="py-lineno"> 490</tt>  <tt class="py-line"><tt class="py-docstring">    &gt;&gt;&gt; options = LogoOptions()</tt> </tt>
<a name="L491"></a><tt class="py-lineno"> 491</tt>  <tt class="py-line"><tt class="py-docstring">    &gt;&gt;&gt; options.title = "A Logo Title"</tt> </tt>
<a name="L492"></a><tt class="py-lineno"> 492</tt>  <tt class="py-line"><tt class="py-docstring">    &gt;&gt;&gt; format = LogoFormat(data, options) </tt> </tt>
<a name="L493"></a><tt class="py-lineno"> 493</tt>  <tt class="py-line"><tt class="py-docstring">    </tt> </tt>
<a name="L494"></a><tt class="py-lineno"> 494</tt>  <tt class="py-line"><tt class="py-docstring">    Raises an ArgumentError if arguments are invalid.</tt> </tt>
<a name="L495"></a><tt class="py-lineno"> 495</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="LogoFormat.__init__"></a><div id="LogoFormat.__init__-def"><a name="L496"></a><tt class="py-lineno"> 496</tt> <a class="py-toggle" href="#" id="LogoFormat.__init__-toggle" onclick="return toggle('LogoFormat.__init__');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="weblogolib.LogoFormat-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">data</tt><tt class="py-op">,</tt> <tt class="py-param">options</tt><tt class="py-op">=</tt> <tt class="py-name">None</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
</div><div id="LogoFormat.__init__-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="LogoFormat.__init__-expanded"><a name="L497"></a><tt class="py-lineno"> 497</tt>  <tt class="py-line">        <tt class="py-docstring">""" Create a new LogoFormat instance.</tt> </tt>
<a name="L498"></a><tt class="py-lineno"> 498</tt>  <tt class="py-line"><tt class="py-docstring">        </tt> </tt>
<a name="L499"></a><tt class="py-lineno"> 499</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L500"></a><tt class="py-lineno"> 500</tt>  <tt class="py-line">        <tt id="link-42" class="py-name" targets="Class weblogolib.LogoOptions=weblogolib.LogoOptions-class.html"><a title="weblogolib.LogoOptions" class="py-name" href="#" onclick="return doclink('link-42', 'LogoOptions', 'link-42');">LogoOptions</a></tt><tt class="py-op">.</tt><tt id="link-43" class="py-name" targets="Method weblogolib.GhostscriptAPI.__init__()=weblogolib.GhostscriptAPI-class.html#__init__,Method weblogolib.LogoData.__init__()=weblogolib.LogoData-class.html#__init__,Method weblogolib.LogoFormat.__init__()=weblogolib.LogoFormat-class.html#__init__,Method weblogolib.LogoOptions.__init__()=weblogolib.LogoOptions-class.html#__init__,Method weblogolib._cgi.Field.__init__()=weblogolib._cgi.Field-class.html#__init__,Method weblogolib.color.Color.__init__()=weblogolib.color.Color-class.html#__init__,Method weblogolib.colorscheme.ColorGroup.__init__()=weblogolib.colorscheme.ColorGroup-class.html#__init__,Method weblogolib.colorscheme.ColorScheme.__init__()=weblogolib.colorscheme.ColorScheme-class.html#__init__,Method weblogolib.logomath.Dirichlet.__init__()=weblogolib.logomath.Dirichlet-class.html#__init__,Method weblogolib.logomath.Gamma.__init__()=weblogolib.logomath.Gamma-class.html#__init__"><a title="weblogolib.GhostscriptAPI.__init__
weblogolib.LogoData.__init__
weblogolib.LogoFormat.__init__
weblogolib.LogoOptions.__init__
weblogolib._cgi.Field.__init__
weblogolib.color.Color.__init__
weblogolib.colorscheme.ColorGroup.__init__
weblogolib.colorscheme.ColorScheme.__init__
weblogolib.logomath.Dirichlet.__init__
weblogolib.logomath.Gamma.__init__" class="py-name" href="#" onclick="return doclink('link-43', '__init__', 'link-43');">__init__</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">)</tt> </tt>
<a name="L501"></a><tt class="py-lineno"> 501</tt>  <tt class="py-line">         </tt>
<a name="L502"></a><tt class="py-lineno"> 502</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">options</tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</tt> <tt class="py-op">:</tt> </tt>
<a name="L503"></a><tt class="py-lineno"> 503</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">__dict__</tt><tt class="py-op">.</tt><tt class="py-name">update</tt><tt class="py-op">(</tt><tt class="py-name">options</tt><tt class="py-op">.</tt><tt class="py-name">__dict__</tt><tt class="py-op">)</tt> </tt>
<a name="L504"></a><tt class="py-lineno"> 504</tt>  <tt class="py-line">                  </tt>
<a name="L505"></a><tt class="py-lineno"> 505</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">alphabet</tt> <tt class="py-op">=</tt> <tt class="py-name">data</tt><tt class="py-op">.</tt><tt class="py-name">alphabet</tt> </tt>
<a name="L506"></a><tt class="py-lineno"> 506</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">seqlen</tt> <tt class="py-op">=</tt> <tt class="py-name">data</tt><tt class="py-op">.</tt><tt class="py-name">length</tt> </tt>
<a name="L507"></a><tt class="py-lineno"> 507</tt>  <tt class="py-line">         </tt>
<a name="L508"></a><tt class="py-lineno"> 508</tt>  <tt class="py-line">         </tt>
<a name="L509"></a><tt class="py-lineno"> 509</tt>  <tt class="py-line">        <tt class="py-comment"># Derived parameters.</tt> </tt>
<a name="L510"></a><tt class="py-lineno"> 510</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">show_title</tt> <tt class="py-op">=</tt> <tt class="py-name">False</tt> </tt>
<a name="L511"></a><tt class="py-lineno"> 511</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">show_xaxis_label</tt> <tt class="py-op">=</tt> <tt class="py-name">False</tt> </tt>
<a name="L512"></a><tt class="py-lineno"> 512</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">yaxis_minor_tic_interval</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L513"></a><tt class="py-lineno"> 513</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">lines_per_logo</tt>       <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L514"></a><tt class="py-lineno"> 514</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">char_width</tt>       <tt class="py-op">=</tt> <tt class="py-name">None</tt>        <tt class="py-comment"># Maximum character width. Stack width minus margins. </tt> </tt>
<a name="L515"></a><tt class="py-lineno"> 515</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">line_margin_left</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L516"></a><tt class="py-lineno"> 516</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">line_margin_right</tt>    <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L517"></a><tt class="py-lineno"> 517</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">line_margin_bottom</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L518"></a><tt class="py-lineno"> 518</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">line_margin_top</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L519"></a><tt class="py-lineno"> 519</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">title_height</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L520"></a><tt class="py-lineno"> 520</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">xaxis_label_height</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L521"></a><tt class="py-lineno"> 521</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">line_height</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L522"></a><tt class="py-lineno"> 522</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">line_width</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L523"></a><tt class="py-lineno"> 523</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">logo_height</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L524"></a><tt class="py-lineno"> 524</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">logo_width</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L525"></a><tt class="py-lineno"> 525</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">creation_date</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L526"></a><tt class="py-lineno"> 526</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">end_type</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L527"></a><tt class="py-lineno"> 527</tt>  <tt class="py-line"> </tt>
<a name="L528"></a><tt class="py-lineno"> 528</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">stack_height</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">stack_width</tt> <tt class="py-op">*</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">stack_aspect_ratio</tt> </tt>
<a name="L529"></a><tt class="py-lineno"> 529</tt>  <tt class="py-line">         </tt>
<a name="L530"></a><tt class="py-lineno"> 530</tt>  <tt class="py-line">        <tt class="py-comment"># Attribute to test, test, error message</tt> </tt>
<a name="L531"></a><tt class="py-lineno"> 531</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-name">arg_conditions</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt> </tt>
<a name="L532"></a><tt class="py-lineno"> 532</tt>  <tt class="py-line">            <tt class="py-op">(</tt><tt class="py-string">"stacks_per_line"</tt><tt class="py-op">,</tt>     <tt class="py-keyword">lambda</tt> <tt class="py-name">x</tt><tt class="py-op">:</tt> <tt class="py-name">x</tt><tt class="py-op">&gt;</tt><tt class="py-number">0</tt> <tt class="py-op">,</tt>     <tt class="py-string">"Stacks per line must be positive."</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L533"></a><tt class="py-lineno"> 533</tt>  <tt class="py-line">            <tt class="py-op">(</tt><tt class="py-string">"stack_width"</tt><tt class="py-op">,</tt>         <tt class="py-keyword">lambda</tt> <tt class="py-name">x</tt><tt class="py-op">:</tt> <tt class="py-name">x</tt><tt class="py-op">&gt;</tt><tt class="py-number">0.0</tt><tt class="py-op">,</tt>    <tt class="py-string">"Stack width must be greater than zero."</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L534"></a><tt class="py-lineno"> 534</tt>  <tt class="py-line">            <tt class="py-op">(</tt><tt class="py-string">"stack_aspect_ratio"</tt> <tt class="py-op">,</tt> <tt class="py-keyword">lambda</tt> <tt class="py-name">x</tt><tt class="py-op">:</tt> <tt class="py-name">x</tt><tt class="py-op">&gt;</tt><tt class="py-number">0</tt><tt class="py-op">,</tt>    <tt class="py-string">"Stack aspect ratio must be greater than zero."</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L535"></a><tt class="py-lineno"> 535</tt>  <tt class="py-line">            <tt class="py-op">(</tt><tt class="py-string">"fontsize"</tt> <tt class="py-op">,</tt>           <tt class="py-keyword">lambda</tt> <tt class="py-name">x</tt><tt class="py-op">:</tt> <tt class="py-name">x</tt><tt class="py-op">&gt;</tt><tt class="py-number">0</tt> <tt class="py-op">,</tt>     <tt class="py-string">"Font sizes must be positive."</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L536"></a><tt class="py-lineno"> 536</tt>  <tt class="py-line">            <tt class="py-op">(</tt><tt class="py-string">"small_fontsize"</tt> <tt class="py-op">,</tt>     <tt class="py-keyword">lambda</tt> <tt class="py-name">x</tt><tt class="py-op">:</tt> <tt class="py-name">x</tt><tt class="py-op">&gt;</tt><tt class="py-number">0</tt> <tt class="py-op">,</tt>     <tt class="py-string">"Font sizes must be positive."</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L537"></a><tt class="py-lineno"> 537</tt>  <tt class="py-line">            <tt class="py-op">(</tt><tt class="py-string">"title_fontsize"</tt> <tt class="py-op">,</tt>     <tt class="py-keyword">lambda</tt> <tt class="py-name">x</tt><tt class="py-op">:</tt> <tt class="py-name">x</tt><tt class="py-op">&gt;</tt><tt class="py-number">0</tt> <tt class="py-op">,</tt>     <tt class="py-string">"Font sizes must be positive."</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L538"></a><tt class="py-lineno"> 538</tt>  <tt class="py-line">            <tt class="py-op">(</tt><tt class="py-string">"errorbar_fraction"</tt> <tt class="py-op">,</tt>  <tt class="py-keyword">lambda</tt> <tt class="py-name">x</tt><tt class="py-op">:</tt> <tt class="py-name">x</tt><tt class="py-op">&gt;=</tt><tt class="py-number">0.0</tt> <tt class="py-keyword">and</tt> <tt class="py-name">x</tt><tt class="py-op">&lt;=</tt><tt class="py-number">1.0</tt><tt class="py-op">,</tt>  </tt>
<a name="L539"></a><tt class="py-lineno"> 539</tt>  <tt class="py-line">                <tt class="py-string">"The visible fraction of the error bar must be between zero and one."</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L540"></a><tt class="py-lineno"> 540</tt>  <tt class="py-line">            <tt class="py-op">(</tt><tt class="py-string">"yaxis_tic_interval"</tt> <tt class="py-op">,</tt> <tt class="py-keyword">lambda</tt> <tt class="py-name">x</tt><tt class="py-op">:</tt> <tt class="py-name">x</tt><tt class="py-op">&gt;=</tt><tt class="py-number">0.0</tt> <tt class="py-op">,</tt> <tt class="py-string">"The yaxis tic interval cannot be negative."</tt><tt class="py-op">)</tt><tt class="py-op">,</tt>                                     </tt>
<a name="L541"></a><tt class="py-lineno"> 541</tt>  <tt class="py-line">            <tt class="py-op">(</tt><tt class="py-string">"yaxis_minor_tic_interval"</tt> <tt class="py-op">,</tt> <tt class="py-keyword">lambda</tt> <tt class="py-name">x</tt><tt class="py-op">:</tt> <tt class="py-keyword">not</tt> <tt class="py-op">(</tt><tt class="py-name">x</tt> <tt class="py-keyword">and</tt> <tt class="py-name">x</tt><tt class="py-op">&lt;</tt><tt class="py-number">0.0</tt><tt class="py-op">)</tt> <tt class="py-op">,</tt> <tt class="py-string">"Distances cannot be negative."</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L542"></a><tt class="py-lineno"> 542</tt>  <tt class="py-line">            <tt class="py-op">(</tt><tt class="py-string">"xaxis_tic_interval"</tt> <tt class="py-op">,</tt> <tt class="py-keyword">lambda</tt> <tt class="py-name">x</tt><tt class="py-op">:</tt> <tt class="py-name">x</tt><tt class="py-op">&gt;</tt><tt class="py-number">0.0</tt> <tt class="py-op">,</tt>   <tt class="py-string">"Tic interval must be greater than zero."</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L543"></a><tt class="py-lineno"> 543</tt>  <tt class="py-line">            <tt class="py-op">(</tt><tt class="py-string">"number_interval"</tt> <tt class="py-op">,</tt>    <tt class="py-keyword">lambda</tt> <tt class="py-name">x</tt><tt class="py-op">:</tt> <tt class="py-name">x</tt><tt class="py-op">&gt;</tt><tt class="py-number">0.0</tt> <tt class="py-op">,</tt>      <tt class="py-string">"Invalid interval between numbers."</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L544"></a><tt class="py-lineno"> 544</tt>  <tt class="py-line">            <tt class="py-op">(</tt><tt class="py-string">"shrink_fraction"</tt> <tt class="py-op">,</tt>    <tt class="py-keyword">lambda</tt> <tt class="py-name">x</tt><tt class="py-op">:</tt> <tt class="py-name">x</tt><tt class="py-op">&gt;=</tt><tt class="py-number">0.0</tt> <tt class="py-keyword">and</tt> <tt class="py-name">x</tt><tt class="py-op">&lt;=</tt><tt class="py-number">1.0</tt> <tt class="py-op">,</tt> <tt class="py-string">"Invalid shrink fraction."</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L545"></a><tt class="py-lineno"> 545</tt>  <tt class="py-line">            <tt class="py-op">(</tt><tt class="py-string">"stack_margin"</tt> <tt class="py-op">,</tt>       <tt class="py-keyword">lambda</tt> <tt class="py-name">x</tt><tt class="py-op">:</tt> <tt class="py-name">x</tt><tt class="py-op">&gt;</tt><tt class="py-number">0.0</tt> <tt class="py-op">,</tt> <tt class="py-string">"Invalid stack margin."</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L546"></a><tt class="py-lineno"> 546</tt>  <tt class="py-line">            <tt class="py-op">(</tt><tt class="py-string">"logo_margin"</tt> <tt class="py-op">,</tt>        <tt class="py-keyword">lambda</tt> <tt class="py-name">x</tt><tt class="py-op">:</tt> <tt class="py-name">x</tt><tt class="py-op">&gt;</tt><tt class="py-number">0.0</tt> <tt class="py-op">,</tt> <tt class="py-string">"Invalid logo margin."</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L547"></a><tt class="py-lineno"> 547</tt>  <tt class="py-line">            <tt class="py-op">(</tt><tt class="py-string">"stroke_width"</tt><tt class="py-op">,</tt>       <tt class="py-keyword">lambda</tt> <tt class="py-name">x</tt><tt class="py-op">:</tt> <tt class="py-name">x</tt><tt class="py-op">&gt;</tt><tt class="py-number">0.0</tt> <tt class="py-op">,</tt> <tt class="py-string">"Invalid stroke width."</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L548"></a><tt class="py-lineno"> 548</tt>  <tt class="py-line">            <tt class="py-op">(</tt><tt class="py-string">"tic_length"</tt> <tt class="py-op">,</tt>         <tt class="py-keyword">lambda</tt> <tt class="py-name">x</tt><tt class="py-op">:</tt> <tt class="py-name">x</tt><tt class="py-op">&gt;</tt><tt class="py-number">0.0</tt> <tt class="py-op">,</tt> <tt class="py-string">"Invalid tic length."</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L549"></a><tt class="py-lineno"> 549</tt>  <tt class="py-line">        <tt class="py-op">)</tt> </tt>
<a name="L550"></a><tt class="py-lineno"> 550</tt>  <tt class="py-line">         </tt>
<a name="L551"></a><tt class="py-lineno"> 551</tt>  <tt class="py-line">        <tt class="py-comment"># Run arguments tests. The second, attribute argument to the ArgumentError is </tt> </tt>
<a name="L552"></a><tt class="py-lineno"> 552</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-comment"># used by the UI to provide user feedback.</tt> </tt>
<a name="L553"></a><tt class="py-lineno"> 553</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-comment"># FIXME: More validation        </tt> </tt>
<a name="L554"></a><tt class="py-lineno"> 554</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-keyword">for</tt> <tt class="py-name">test</tt> <tt class="py-keyword">in</tt> <tt class="py-name">arg_conditions</tt> <tt class="py-op">:</tt> </tt>
<a name="L555"></a><tt class="py-lineno"> 555</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">test</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">(</tt> <tt class="py-name">getattr</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt><tt class="py-name">test</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> <tt class="py-op">)</tt> <tt class="py-op">:</tt> <tt class="py-keyword">raise</tt> <tt class="py-name">ArgumentError</tt><tt class="py-op">(</tt><tt class="py-name">test</tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">test</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L556"></a><tt class="py-lineno"> 556</tt>  <tt class="py-line">    </tt>
<a name="L557"></a><tt class="py-lineno"> 557</tt>  <tt class="py-line">          </tt>
<a name="L558"></a><tt class="py-lineno"> 558</tt>  <tt class="py-line">        <tt class="py-comment"># Inclusive upper and lower bounds</tt> </tt>
<a name="L559"></a><tt class="py-lineno"> 559</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-comment"># FIXME: Validate here. Move from eps_formatter        </tt> </tt>
<a name="L560"></a><tt class="py-lineno"> 560</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">logo_start</tt> <tt class="py-keyword">is</tt>  <tt class="py-name">None</tt><tt class="py-op">:</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">logo_start</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">first_index</tt> </tt>
<a name="L561"></a><tt class="py-lineno"> 561</tt>  <tt class="py-line">         </tt>
<a name="L562"></a><tt class="py-lineno"> 562</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">logo_end</tt> <tt class="py-keyword">is</tt>  <tt class="py-name">None</tt> <tt class="py-op">:</tt>  </tt>
<a name="L563"></a><tt class="py-lineno"> 563</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">logo_end</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">seqlen</tt> <tt class="py-op">+</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">first_index</tt> <tt class="py-op">-</tt><tt class="py-number">1</tt>  </tt>
<a name="L564"></a><tt class="py-lineno"> 564</tt>  <tt class="py-line">         </tt>
<a name="L565"></a><tt class="py-lineno"> 565</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">total_stacks</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">logo_end</tt> <tt class="py-op">-</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">logo_start</tt> <tt class="py-op">+</tt><tt class="py-number">1</tt> </tt>
<a name="L566"></a><tt class="py-lineno"> 566</tt>  <tt class="py-line"> </tt>
<a name="L567"></a><tt class="py-lineno"> 567</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">logo_start</tt> <tt class="py-op">-</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">first_index</tt> <tt class="py-op">&lt;</tt><tt class="py-number">0</tt> <tt class="py-op">:</tt> </tt>
<a name="L568"></a><tt class="py-lineno"> 568</tt>  <tt class="py-line">            <tt class="py-keyword">raise</tt> <tt class="py-name">ArgumentError</tt><tt class="py-op">(</tt> </tt>
<a name="L569"></a><tt class="py-lineno"> 569</tt>  <tt class="py-line">                <tt class="py-string">"Logo range extends before start of available sequence."</tt><tt class="py-op">,</tt> </tt>
<a name="L570"></a><tt class="py-lineno"> 570</tt>  <tt class="py-line">                <tt class="py-string">'logo_range'</tt><tt class="py-op">)</tt> </tt>
<a name="L571"></a><tt class="py-lineno"> 571</tt>  <tt class="py-line">         </tt>
<a name="L572"></a><tt class="py-lineno"> 572</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">logo_end</tt> <tt class="py-op">-</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">first_index</tt>  <tt class="py-op">&gt;=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">seqlen</tt>  <tt class="py-op">:</tt>  </tt>
<a name="L573"></a><tt class="py-lineno"> 573</tt>  <tt class="py-line">            <tt class="py-keyword">raise</tt> <tt class="py-name">ArgumentError</tt><tt class="py-op">(</tt> </tt>
<a name="L574"></a><tt class="py-lineno"> 574</tt>  <tt class="py-line">                <tt class="py-string">"Logo range extends beyond end of available sequence."</tt><tt class="py-op">,</tt> </tt>
<a name="L575"></a><tt class="py-lineno"> 575</tt>  <tt class="py-line">                <tt class="py-string">'logo_range'</tt><tt class="py-op">)</tt> </tt>
<a name="L576"></a><tt class="py-lineno"> 576</tt>  <tt class="py-line">     </tt>
<a name="L577"></a><tt class="py-lineno"> 577</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">logo_title</tt>      <tt class="py-op">:</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">show_title</tt> <tt class="py-op">=</tt> <tt class="py-name">True</tt> </tt>
<a name="L578"></a><tt class="py-lineno"> 578</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">fineprint</tt>   <tt class="py-op">:</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">show_fineprint</tt> <tt class="py-op">=</tt> <tt class="py-name">False</tt> </tt>
<a name="L579"></a><tt class="py-lineno"> 579</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">xaxis_label</tt>     <tt class="py-op">:</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">show_xaxis_label</tt> <tt class="py-op">=</tt> <tt class="py-name">True</tt> </tt>
<a name="L580"></a><tt class="py-lineno"> 580</tt>  <tt class="py-line"> </tt>
<a name="L581"></a><tt class="py-lineno"> 581</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">yaxis_label</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt> <tt class="py-op">:</tt>  </tt>
<a name="L582"></a><tt class="py-lineno"> 582</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">yaxis_label</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">unit_name</tt> </tt>
<a name="L583"></a><tt class="py-lineno"> 583</tt>  <tt class="py-line">         </tt>
<a name="L584"></a><tt class="py-lineno"> 584</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">yaxis_label</tt> <tt class="py-op">:</tt>  </tt>
<a name="L585"></a><tt class="py-lineno"> 585</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">show_yaxis_label</tt> <tt class="py-op">=</tt> <tt class="py-name">True</tt> </tt>
<a name="L586"></a><tt class="py-lineno"> 586</tt>  <tt class="py-line">        <tt class="py-keyword">else</tt> <tt class="py-op">:</tt> </tt>
<a name="L587"></a><tt class="py-lineno"> 587</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">show_yaxis_label</tt> <tt class="py-op">=</tt> <tt class="py-name">False</tt> </tt>
<a name="L588"></a><tt class="py-lineno"> 588</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">show_ends</tt> <tt class="py-op">=</tt> <tt class="py-name">False</tt> </tt>
<a name="L589"></a><tt class="py-lineno"> 589</tt>  <tt class="py-line">               </tt>
<a name="L590"></a><tt class="py-lineno"> 590</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">yaxis_scale</tt> <tt class="py-op">:</tt> </tt>
<a name="L591"></a><tt class="py-lineno"> 591</tt>  <tt class="py-line">            <tt class="py-name">conversion_factor</tt> <tt class="py-op">=</tt> <tt id="link-44" class="py-name"><a title="weblogolib.std_units" class="py-name" href="#" onclick="return doclink('link-44', 'std_units', 'link-34');">std_units</a></tt><tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">unit_name</tt><tt class="py-op">]</tt> </tt>
<a name="L592"></a><tt class="py-lineno"> 592</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">conversion_factor</tt> <tt class="py-op">:</tt> </tt>
<a name="L593"></a><tt class="py-lineno"> 593</tt>  <tt class="py-line">                <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">yaxis_scale</tt><tt class="py-op">=</tt><tt class="py-name">log</tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">alphabet</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-name">conversion_factor</tt> </tt>
<a name="L594"></a><tt class="py-lineno"> 594</tt>  <tt class="py-line">            <tt class="py-keyword">else</tt> <tt class="py-op">:</tt> </tt>
<a name="L595"></a><tt class="py-lineno"> 595</tt>  <tt class="py-line">                <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">yaxis_scale</tt><tt class="py-op">=</tt><tt class="py-number">1.0</tt>    <tt class="py-comment"># probability units</tt> </tt>
<a name="L596"></a><tt class="py-lineno"> 596</tt>  <tt class="py-line"> </tt>
<a name="L597"></a><tt class="py-lineno"> 597</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">yaxis_scale</tt><tt class="py-op">&lt;=</tt><tt class="py-number">0.0</tt> <tt class="py-op">:</tt>  </tt>
<a name="L598"></a><tt class="py-lineno"> 598</tt>  <tt class="py-line">            <tt class="py-keyword">raise</tt> <tt class="py-name">ArgumentError</tt><tt class="py-op">(</tt><tt class="py-string">"Invalid yaxis scale"</tt><tt class="py-op">,</tt> <tt class="py-string">'yaxis_scale'</tt><tt class="py-op">,</tt><tt class="py-op">)</tt> </tt>
<a name="L599"></a><tt class="py-lineno"> 599</tt>  <tt class="py-line"> </tt>
<a name="L600"></a><tt class="py-lineno"> 600</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">yaxis_tic_interval</tt> <tt class="py-op">&gt;=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">yaxis_scale</tt><tt class="py-op">:</tt> </tt>
<a name="L601"></a><tt class="py-lineno"> 601</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">yaxis_tic_interval</tt> <tt class="py-op">/=</tt> <tt class="py-number">2.</tt>  </tt>
<a name="L602"></a><tt class="py-lineno"> 602</tt>  <tt class="py-line"> </tt>
<a name="L603"></a><tt class="py-lineno"> 603</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">yaxis_minor_tic_interval</tt> \ </tt>
<a name="L604"></a><tt class="py-lineno"> 604</tt>  <tt class="py-line">            <tt class="py-op">=</tt> <tt class="py-name">float</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">yaxis_tic_interval</tt><tt class="py-op">)</tt><tt class="py-op">/</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">yaxis_minor_tic_ratio</tt> </tt>
<a name="L605"></a><tt class="py-lineno"> 605</tt>  <tt class="py-line">                       </tt>
<a name="L606"></a><tt class="py-lineno"> 606</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">color_scheme</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt> <tt class="py-op">:</tt> </tt>
<a name="L607"></a><tt class="py-lineno"> 607</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">alphabet</tt> <tt class="py-keyword">in</tt> <tt id="link-45" class="py-name"><a title="weblogolib.default_color_schemes" class="py-name" href="#" onclick="return doclink('link-45', 'default_color_schemes', 'link-30');">default_color_schemes</a></tt> <tt class="py-op">:</tt> </tt>
<a name="L608"></a><tt class="py-lineno"> 608</tt>  <tt class="py-line">                <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">color_scheme</tt> <tt class="py-op">=</tt> <tt id="link-46" class="py-name"><a title="weblogolib.default_color_schemes" class="py-name" href="#" onclick="return doclink('link-46', 'default_color_schemes', 'link-30');">default_color_schemes</a></tt><tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">alphabet</tt><tt class="py-op">]</tt> </tt>
<a name="L609"></a><tt class="py-lineno"> 609</tt>  <tt class="py-line">            <tt class="py-keyword">else</tt> <tt class="py-op">:</tt> </tt>
<a name="L610"></a><tt class="py-lineno"> 610</tt>  <tt class="py-line">                <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">color_scheme</tt> <tt class="py-op">=</tt> <tt id="link-47" class="py-name"><a title="weblogolib.colorscheme.monochrome" class="py-name" href="#" onclick="return doclink('link-47', 'monochrome', 'link-24');">monochrome</a></tt> </tt>
<a name="L611"></a><tt class="py-lineno"> 611</tt>  <tt class="py-line"> </tt>
<a name="L612"></a><tt class="py-lineno"> 612</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">lines_per_logo</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt><tt class="py-op">+</tt> <tt class="py-op">(</tt> <tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">total_stacks</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> <tt class="py-op">/</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">stacks_per_line</tt><tt class="py-op">)</tt> </tt>
<a name="L613"></a><tt class="py-lineno"> 613</tt>  <tt class="py-line">     </tt>
<a name="L614"></a><tt class="py-lineno"> 614</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">lines_per_logo</tt><tt class="py-op">==</tt><tt class="py-number">1</tt> <tt class="py-keyword">and</tt> <tt class="py-keyword">not</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">pad_right</tt><tt class="py-op">:</tt> </tt>
<a name="L615"></a><tt class="py-lineno"> 615</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">stacks_per_line</tt> <tt class="py-op">=</tt> <tt class="py-name">min</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">stacks_per_line</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">total_stacks</tt><tt class="py-op">)</tt> </tt>
<a name="L616"></a><tt class="py-lineno"> 616</tt>  <tt class="py-line"> </tt>
<a name="L617"></a><tt class="py-lineno"> 617</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">char_width</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">stack_width</tt> <tt class="py-op">-</tt> <tt class="py-number">2</tt><tt class="py-op">*</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">stack_margin</tt> </tt>
<a name="L618"></a><tt class="py-lineno"> 618</tt>  <tt class="py-line">     </tt>
<a name="L619"></a><tt class="py-lineno"> 619</tt>  <tt class="py-line">     </tt>
<a name="L620"></a><tt class="py-lineno"> 620</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">show_yaxis</tt> <tt class="py-op">:</tt> </tt>
<a name="L621"></a><tt class="py-lineno"> 621</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">line_margin_left</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">fontsize</tt> <tt class="py-op">*</tt> <tt class="py-number">3.0</tt> </tt>
<a name="L622"></a><tt class="py-lineno"> 622</tt>  <tt class="py-line">        <tt class="py-keyword">else</tt> <tt class="py-op">:</tt> </tt>
<a name="L623"></a><tt class="py-lineno"> 623</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">line_margin_left</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L624"></a><tt class="py-lineno"> 624</tt>  <tt class="py-line"> </tt>
<a name="L625"></a><tt class="py-lineno"> 625</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">show_ends</tt> <tt class="py-op">:</tt> </tt>
<a name="L626"></a><tt class="py-lineno"> 626</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">line_margin_right</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">fontsize</tt> <tt class="py-op">*</tt><tt class="py-number">1.5</tt>  </tt>
<a name="L627"></a><tt class="py-lineno"> 627</tt>  <tt class="py-line">        <tt class="py-keyword">else</tt> <tt class="py-op">:</tt> </tt>
<a name="L628"></a><tt class="py-lineno"> 628</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">line_margin_right</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">fontsize</tt>              </tt>
<a name="L629"></a><tt class="py-lineno"> 629</tt>  <tt class="py-line"> </tt>
<a name="L630"></a><tt class="py-lineno"> 630</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">show_xaxis</tt> <tt class="py-op">:</tt> </tt>
<a name="L631"></a><tt class="py-lineno"> 631</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">rotate_numbers</tt> <tt class="py-op">:</tt> </tt>
<a name="L632"></a><tt class="py-lineno"> 632</tt>  <tt class="py-line">                <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">line_margin_bottom</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">number_fontsize</tt> <tt class="py-op">*</tt><tt class="py-number">2.5</tt> </tt>
<a name="L633"></a><tt class="py-lineno"> 633</tt>  <tt class="py-line">            <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L634"></a><tt class="py-lineno"> 634</tt>  <tt class="py-line">                <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">line_margin_bottom</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">number_fontsize</tt> <tt class="py-op">*</tt><tt class="py-number">1.5</tt> </tt>
<a name="L635"></a><tt class="py-lineno"> 635</tt>  <tt class="py-line">        <tt class="py-keyword">else</tt> <tt class="py-op">:</tt> </tt>
<a name="L636"></a><tt class="py-lineno"> 636</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">line_margin_bottom</tt> <tt class="py-op">=</tt> <tt class="py-number">4</tt> </tt>
<a name="L637"></a><tt class="py-lineno"> 637</tt>  <tt class="py-line"> </tt>
<a name="L638"></a><tt class="py-lineno"> 638</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">line_margin_top</tt> <tt class="py-op">=</tt> <tt class="py-number">4</tt> </tt>
<a name="L639"></a><tt class="py-lineno"> 639</tt>  <tt class="py-line">     </tt>
<a name="L640"></a><tt class="py-lineno"> 640</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">show_title</tt> <tt class="py-op">:</tt> </tt>
<a name="L641"></a><tt class="py-lineno"> 641</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">title_height</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">title_fontsize</tt>  </tt>
<a name="L642"></a><tt class="py-lineno"> 642</tt>  <tt class="py-line">        <tt class="py-keyword">else</tt> <tt class="py-op">:</tt> </tt>
<a name="L643"></a><tt class="py-lineno"> 643</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">title_height</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L644"></a><tt class="py-lineno"> 644</tt>  <tt class="py-line"> </tt>
<a name="L645"></a><tt class="py-lineno"> 645</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">xaxis_label_height</tt> <tt class="py-op">=</tt><tt class="py-number">0.</tt> </tt>
<a name="L646"></a><tt class="py-lineno"> 646</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">show_xaxis_label</tt> <tt class="py-op">:</tt> </tt>
<a name="L647"></a><tt class="py-lineno"> 647</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">xaxis_label_height</tt> <tt class="py-op">+=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">fontsize</tt> </tt>
<a name="L648"></a><tt class="py-lineno"> 648</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">show_fineprint</tt> <tt class="py-op">:</tt> </tt>
<a name="L649"></a><tt class="py-lineno"> 649</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">xaxis_label_height</tt> <tt class="py-op">+=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">small_fontsize</tt> </tt>
<a name="L650"></a><tt class="py-lineno"> 650</tt>  <tt class="py-line"> </tt>
<a name="L651"></a><tt class="py-lineno"> 651</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">line_height</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">stack_height</tt> <tt class="py-op">+</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">line_margin_top</tt> <tt class="py-op">+</tt>     </tt>
<a name="L652"></a><tt class="py-lineno"> 652</tt>  <tt class="py-line">                            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">line_margin_bottom</tt> <tt class="py-op">)</tt> </tt>
<a name="L653"></a><tt class="py-lineno"> 653</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">line_width</tt>  <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">stack_width</tt><tt class="py-op">*</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">stacks_per_line</tt> <tt class="py-op">+</tt>  </tt>
<a name="L654"></a><tt class="py-lineno"> 654</tt>  <tt class="py-line">                            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">line_margin_left</tt> <tt class="py-op">+</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">line_margin_right</tt> <tt class="py-op">)</tt> </tt>
<a name="L655"></a><tt class="py-lineno"> 655</tt>  <tt class="py-line"> </tt>
<a name="L656"></a><tt class="py-lineno"> 656</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">logo_height</tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-number">2</tt><tt class="py-op">*</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">logo_margin</tt> <tt class="py-op">+</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">title_height</tt> \ </tt>
<a name="L657"></a><tt class="py-lineno"> 657</tt>  <tt class="py-line">            <tt class="py-op">+</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">xaxis_label_height</tt> <tt class="py-op">+</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">line_height</tt><tt class="py-op">*</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">lines_per_logo</tt><tt class="py-op">)</tt>  </tt>
<a name="L658"></a><tt class="py-lineno"> 658</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">logo_width</tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-number">2</tt><tt class="py-op">*</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">logo_margin</tt> <tt class="py-op">+</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">line_width</tt> <tt class="py-op">)</tt> </tt>
<a name="L659"></a><tt class="py-lineno"> 659</tt>  <tt class="py-line"> </tt>
<a name="L660"></a><tt class="py-lineno"> 660</tt>  <tt class="py-line"> </tt>
<a name="L661"></a><tt class="py-lineno"> 661</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">creation_date</tt> <tt class="py-op">=</tt> <tt class="py-name">datetime</tt><tt class="py-op">.</tt><tt class="py-name">now</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">isoformat</tt><tt class="py-op">(</tt><tt class="py-string">' '</tt><tt class="py-op">)</tt>  </tt>
<a name="L662"></a><tt class="py-lineno"> 662</tt>  <tt class="py-line"> </tt>
<a name="L663"></a><tt class="py-lineno"> 663</tt>  <tt class="py-line">        <tt class="py-name">end_type</tt> <tt class="py-op">=</tt> <tt class="py-string">'-'</tt> </tt>
<a name="L664"></a><tt class="py-lineno"> 664</tt>  <tt class="py-line">        <tt class="py-name">end_types</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt> </tt>
<a name="L665"></a><tt class="py-lineno"> 665</tt>  <tt class="py-line">            <tt class="py-name">unambiguous_protein_alphabet</tt><tt class="py-op">:</tt> <tt class="py-string">'p'</tt><tt class="py-op">,</tt>  </tt>
<a name="L666"></a><tt class="py-lineno"> 666</tt>  <tt class="py-line">            <tt class="py-name">unambiguous_rna_alphabet</tt><tt class="py-op">:</tt> <tt class="py-string">'-'</tt><tt class="py-op">,</tt> </tt>
<a name="L667"></a><tt class="py-lineno"> 667</tt>  <tt class="py-line">            <tt class="py-name">unambiguous_dna_alphabet</tt><tt class="py-op">:</tt> <tt class="py-string">'d'</tt>  </tt>
<a name="L668"></a><tt class="py-lineno"> 668</tt>  <tt class="py-line">        <tt class="py-op">}</tt> </tt>
<a name="L669"></a><tt class="py-lineno"> 669</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">show_ends</tt> <tt class="py-keyword">and</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">alphabet</tt> <tt class="py-keyword">in</tt> <tt class="py-name">end_types</tt><tt class="py-op">:</tt> </tt>
<a name="L670"></a><tt class="py-lineno"> 670</tt>  <tt class="py-line">            <tt class="py-name">end_type</tt> <tt class="py-op">=</tt> <tt class="py-name">end_types</tt><tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">alphabet</tt><tt class="py-op">]</tt> </tt>
<a name="L671"></a><tt class="py-lineno"> 671</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">end_type</tt> <tt class="py-op">=</tt> <tt class="py-name">end_type</tt> </tt>
<a name="L672"></a><tt class="py-lineno"> 672</tt>  <tt class="py-line"> </tt>
<a name="L673"></a><tt class="py-lineno"> 673</tt>  <tt class="py-line">         </tt>
<a name="L674"></a><tt class="py-lineno"> 674</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">annotate</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt> <tt class="py-op">:</tt> </tt>
<a name="L675"></a><tt class="py-lineno"> 675</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">annotate</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L676"></a><tt class="py-lineno"> 676</tt>  <tt class="py-line">            <tt class="py-keyword">for</tt> <tt class="py-name">i</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">seqlen</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L677"></a><tt class="py-lineno"> 677</tt>  <tt class="py-line">                <tt class="py-name">index</tt> <tt class="py-op">=</tt> <tt class="py-name">i</tt> <tt class="py-op">+</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">first_index</tt> </tt>
<a name="L678"></a><tt class="py-lineno"> 678</tt>  <tt class="py-line">                <tt class="py-keyword">if</tt> <tt class="py-name">index</tt> <tt class="py-op">%</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">number_interval</tt> <tt class="py-op">==</tt> <tt class="py-number">0</tt> <tt class="py-op">:</tt>  </tt>
<a name="L679"></a><tt class="py-lineno"> 679</tt>  <tt class="py-line">                    <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">annotate</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt> <tt class="py-string">"%d"</tt><tt class="py-op">%</tt><tt class="py-name">index</tt><tt class="py-op">)</tt> </tt>
<a name="L680"></a><tt class="py-lineno"> 680</tt>  <tt class="py-line">                <tt class="py-keyword">else</tt> <tt class="py-op">:</tt> </tt>
<a name="L681"></a><tt class="py-lineno"> 681</tt>  <tt class="py-line">                    <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">annotate</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-string">""</tt><tt class="py-op">)</tt> </tt>
<a name="L682"></a><tt class="py-lineno"> 682</tt>  <tt class="py-line">                     </tt>
<a name="L683"></a><tt class="py-lineno"> 683</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">annotate</tt><tt class="py-op">)</tt><tt class="py-op">!=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">seqlen</tt>  <tt class="py-op">:</tt> </tt>
<a name="L684"></a><tt class="py-lineno"> 684</tt>  <tt class="py-line">            <tt class="py-keyword">raise</tt> <tt class="py-name">ArgumentError</tt><tt class="py-op">(</tt> </tt>
<a name="L685"></a><tt class="py-lineno"> 685</tt>  <tt class="py-line">                  <tt class="py-string">"Annotations must be same length as sequences."</tt><tt class="py-op">,</tt> </tt>
<a name="L686"></a><tt class="py-lineno"> 686</tt>  <tt class="py-line">                  <tt class="py-string">'annotate'</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L687"></a><tt class="py-lineno"> 687</tt>  <tt class="py-line">             </tt>
<a name="pdf_formatter"></a><div id="pdf_formatter-def"><a name="L688"></a><tt class="py-lineno"> 688</tt>  <tt class="py-line"> </tt>
<a name="L689"></a><tt class="py-lineno"> 689</tt>  <tt class="py-line">    <tt class="py-comment"># End __init__</tt> </tt>
<a name="L690"></a><tt class="py-lineno"> 690</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># End class LogoFormat</tt> </tt>
<a name="L691"></a><tt class="py-lineno"> 691</tt>  <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L692"></a><tt class="py-lineno"> 692</tt>  <tt class="py-line"> </tt>
<a name="L693"></a><tt class="py-lineno"> 693</tt>  <tt class="py-line"> </tt>
<a name="L694"></a><tt class="py-lineno"> 694</tt>  <tt class="py-line"><tt class="py-comment"># ------ Logo Formaters ------</tt> </tt>
<a name="L695"></a><tt class="py-lineno"> 695</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># Each formatter is a function f(LogoData, LogoFormat, output file).</tt> </tt>
<a name="L696"></a><tt class="py-lineno"> 696</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># that draws a representation of the logo into the given file.</tt> </tt>
<a name="L697"></a><tt class="py-lineno"> 697</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># The main graphical formatter is eps_formatter. A mapping 'formatters'</tt> </tt>
<a name="L698"></a><tt class="py-lineno"> 698</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># containing all available formatters is located after the formatter</tt> </tt>
<a name="L699"></a><tt class="py-lineno"> 699</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># definitions. </tt> </tt>
<a name="L700"></a><tt class="py-lineno"> 700</tt>  <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L701"></a><tt class="py-lineno"> 701</tt> <a class="py-toggle" href="#" id="pdf_formatter-toggle" onclick="return toggle('pdf_formatter');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="weblogolib-module.html#pdf_formatter">pdf_formatter</a><tt class="py-op">(</tt><tt class="py-param">data</tt><tt class="py-op">,</tt> <tt class="py-param">format</tt><tt class="py-op">,</tt> <tt class="py-param">fout</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
</div><div id="pdf_formatter-collapsed" style="display:none;" pad="++++" indent="++++"></div><div id="pdf_formatter-expanded"><a name="L702"></a><tt class="py-lineno"> 702</tt>  <tt class="py-line">    <tt class="py-docstring">""" Generate a logo in PDF format."""</tt> </tt>
<a name="L703"></a><tt class="py-lineno"> 703</tt>  <tt class="py-line">     </tt>
<a name="L704"></a><tt class="py-lineno"> 704</tt>  <tt class="py-line">    <tt class="py-name">feps</tt> <tt class="py-op">=</tt> <tt class="py-name">StringIO</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L705"></a><tt class="py-lineno"> 705</tt>  <tt class="py-line">    <tt id="link-48" class="py-name" targets="Function weblogolib.eps_formatter()=weblogolib-module.html#eps_formatter"><a title="weblogolib.eps_formatter" class="py-name" href="#" onclick="return doclink('link-48', 'eps_formatter', 'link-48');">eps_formatter</a></tt><tt class="py-op">(</tt><tt class="py-name">data</tt><tt class="py-op">,</tt> <tt class="py-name">format</tt><tt class="py-op">,</tt> <tt class="py-name">feps</tt><tt class="py-op">)</tt> </tt>
<a name="L706"></a><tt class="py-lineno"> 706</tt>  <tt class="py-line">    <tt class="py-name">feps</tt><tt class="py-op">.</tt><tt class="py-name">seek</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">)</tt> </tt>
<a name="L707"></a><tt class="py-lineno"> 707</tt>  <tt class="py-line">     </tt>
<a name="L708"></a><tt class="py-lineno"> 708</tt>  <tt class="py-line">    <tt class="py-name">gs</tt> <tt class="py-op">=</tt> <tt id="link-49" class="py-name" targets="Class weblogolib.GhostscriptAPI=weblogolib.GhostscriptAPI-class.html"><a title="weblogolib.GhostscriptAPI" class="py-name" href="#" onclick="return doclink('link-49', 'GhostscriptAPI', 'link-49');">GhostscriptAPI</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt>     </tt>
<a name="L709"></a><tt class="py-lineno"> 709</tt>  <tt class="py-line">    <tt class="py-name">gs</tt><tt class="py-op">.</tt><tt id="link-50" class="py-name" targets="Method weblogolib.GhostscriptAPI.convert()=weblogolib.GhostscriptAPI-class.html#convert"><a title="weblogolib.GhostscriptAPI.convert" class="py-name" href="#" onclick="return doclink('link-50', 'convert', 'link-50');">convert</a></tt><tt class="py-op">(</tt><tt class="py-string">'pdf'</tt><tt class="py-op">,</tt> <tt class="py-name">feps</tt><tt class="py-op">,</tt> <tt class="py-name">fout</tt><tt class="py-op">,</tt> <tt class="py-name">format</tt><tt class="py-op">.</tt><tt class="py-name">logo_width</tt><tt class="py-op">,</tt> <tt class="py-name">format</tt><tt class="py-op">.</tt><tt class="py-name">logo_height</tt><tt class="py-op">)</tt> </tt>
</div><a name="L710"></a><tt class="py-lineno"> 710</tt>  <tt class="py-line"> </tt>
<a name="_bitmap_formatter"></a><div id="_bitmap_formatter-def"><a name="L711"></a><tt class="py-lineno"> 711</tt>  <tt class="py-line"> </tt>
<a name="L712"></a><tt class="py-lineno"> 712</tt> <a class="py-toggle" href="#" id="_bitmap_formatter-toggle" onclick="return toggle('_bitmap_formatter');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="weblogolib-module.html#_bitmap_formatter">_bitmap_formatter</a><tt class="py-op">(</tt><tt class="py-param">data</tt><tt class="py-op">,</tt> <tt class="py-param">format</tt><tt class="py-op">,</tt> <tt class="py-param">fout</tt><tt class="py-op">,</tt> <tt class="py-param">device</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
</div><div id="_bitmap_formatter-collapsed" style="display:none;" pad="++++" indent="++++"></div><div id="_bitmap_formatter-expanded"><a name="L713"></a><tt class="py-lineno"> 713</tt>  <tt class="py-line">    <tt class="py-name">feps</tt> <tt class="py-op">=</tt> <tt class="py-name">StringIO</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L714"></a><tt class="py-lineno"> 714</tt>  <tt class="py-line">    <tt id="link-51" class="py-name"><a title="weblogolib.eps_formatter" class="py-name" href="#" onclick="return doclink('link-51', 'eps_formatter', 'link-48');">eps_formatter</a></tt><tt class="py-op">(</tt><tt class="py-name">data</tt><tt class="py-op">,</tt> <tt class="py-name">format</tt><tt class="py-op">,</tt> <tt class="py-name">feps</tt><tt class="py-op">)</tt> </tt>
<a name="L715"></a><tt class="py-lineno"> 715</tt>  <tt class="py-line">    <tt class="py-name">feps</tt><tt class="py-op">.</tt><tt class="py-name">seek</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">)</tt> </tt>
<a name="L716"></a><tt class="py-lineno"> 716</tt>  <tt class="py-line">     </tt>
<a name="L717"></a><tt class="py-lineno"> 717</tt>  <tt class="py-line">    <tt class="py-name">gs</tt> <tt class="py-op">=</tt> <tt id="link-52" class="py-name"><a title="weblogolib.GhostscriptAPI" class="py-name" href="#" onclick="return doclink('link-52', 'GhostscriptAPI', 'link-49');">GhostscriptAPI</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt>     </tt>
<a name="L718"></a><tt class="py-lineno"> 718</tt>  <tt class="py-line">    <tt class="py-name">gs</tt><tt class="py-op">.</tt><tt id="link-53" class="py-name"><a title="weblogolib.GhostscriptAPI.convert" class="py-name" href="#" onclick="return doclink('link-53', 'convert', 'link-50');">convert</a></tt><tt class="py-op">(</tt><tt class="py-name">device</tt><tt class="py-op">,</tt> <tt class="py-name">feps</tt><tt class="py-op">,</tt> <tt class="py-name">fout</tt><tt class="py-op">,</tt>  </tt>
<a name="L719"></a><tt class="py-lineno"> 719</tt>  <tt class="py-line">        <tt class="py-name">format</tt><tt class="py-op">.</tt><tt class="py-name">logo_width</tt><tt class="py-op">,</tt> <tt class="py-name">format</tt><tt class="py-op">.</tt><tt class="py-name">logo_height</tt><tt class="py-op">,</tt> <tt class="py-name">format</tt><tt class="py-op">.</tt><tt class="py-name">resolution</tt><tt class="py-op">)</tt> </tt>
</div><a name="L720"></a><tt class="py-lineno"> 720</tt>  <tt class="py-line"> </tt>
<a name="jpeg_formatter"></a><div id="jpeg_formatter-def"><a name="L721"></a><tt class="py-lineno"> 721</tt>  <tt class="py-line"> </tt>
<a name="L722"></a><tt class="py-lineno"> 722</tt> <a class="py-toggle" href="#" id="jpeg_formatter-toggle" onclick="return toggle('jpeg_formatter');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="weblogolib-module.html#jpeg_formatter">jpeg_formatter</a><tt class="py-op">(</tt><tt class="py-param">data</tt><tt class="py-op">,</tt> <tt class="py-param">format</tt><tt class="py-op">,</tt> <tt class="py-param">fout</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt>  </tt>
</div><a name="L723"></a><tt class="py-lineno"> 723</tt>  <tt class="py-line">    <tt class="py-docstring">""" Generate a logo in JPEG format."""</tt> </tt>
<a name="L724"></a><tt class="py-lineno"> 724</tt>  <tt class="py-line">    <tt class="py-name">_bitmap_formatter</tt><tt class="py-op">(</tt><tt class="py-name">data</tt><tt class="py-op">,</tt> <tt class="py-name">format</tt><tt class="py-op">,</tt> <tt class="py-name">fout</tt><tt class="py-op">,</tt> <tt class="py-name">device</tt><tt class="py-op">=</tt><tt class="py-string">"jpeg"</tt><tt class="py-op">)</tt> </tt>
</div><a name="L725"></a><tt class="py-lineno"> 725</tt>  <tt class="py-line"> </tt>
<a name="svg_formatter"></a><div id="svg_formatter-def"><a name="L726"></a><tt class="py-lineno"> 726</tt> <a class="py-toggle" href="#" id="svg_formatter-toggle" onclick="return toggle('svg_formatter');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="weblogolib-module.html#svg_formatter">svg_formatter</a><tt class="py-op">(</tt><tt class="py-param">data</tt><tt class="py-op">,</tt> <tt class="py-param">format</tt><tt class="py-op">,</tt> <tt class="py-param">fout</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt>  </tt>
</div><a name="L727"></a><tt class="py-lineno"> 727</tt>  <tt class="py-line">    <tt class="py-docstring">""" Generate a logo in Scalable Vector Graphics (SVG) format.</tt> </tt>
<a name="L728"></a><tt class="py-lineno"> 728</tt>  <tt class="py-line"><tt class="py-docstring">    Requires the program 'pdf2svg' be installed.</tt> </tt>
<a name="L729"></a><tt class="py-lineno"> 729</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L730"></a><tt class="py-lineno"> 730</tt>  <tt class="py-line"> </tt>
<a name="L731"></a><tt class="py-lineno"> 731</tt>  <tt class="py-line">    <tt class="py-name">fpdf</tt> <tt class="py-op">=</tt> <tt class="py-name">StringIO</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L732"></a><tt class="py-lineno"> 732</tt>  <tt class="py-line">    <tt id="link-54" class="py-name" targets="Function weblogolib.pdf_formatter()=weblogolib-module.html#pdf_formatter"><a title="weblogolib.pdf_formatter" class="py-name" href="#" onclick="return doclink('link-54', 'pdf_formatter', 'link-54');">pdf_formatter</a></tt><tt class="py-op">(</tt><tt class="py-name">data</tt><tt class="py-op">,</tt> <tt class="py-name">format</tt><tt class="py-op">,</tt> <tt class="py-name">fpdf</tt><tt class="py-op">)</tt> </tt>
<a name="L733"></a><tt class="py-lineno"> 733</tt>  <tt class="py-line">    <tt class="py-name">fpdf</tt><tt class="py-op">.</tt><tt class="py-name">seek</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">)</tt> </tt>
<a name="L734"></a><tt class="py-lineno"> 734</tt>  <tt class="py-line">     </tt>
<a name="L735"></a><tt class="py-lineno"> 735</tt>  <tt class="py-line">    <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L736"></a><tt class="py-lineno"> 736</tt>  <tt class="py-line">            <tt class="py-name">command</tt> <tt class="py-op">=</tt> <tt class="py-name">find_command</tt><tt class="py-op">(</tt><tt class="py-string">'pdf2svg'</tt><tt class="py-op">)</tt>  </tt>
<a name="L737"></a><tt class="py-lineno"> 737</tt>  <tt class="py-line">    <tt class="py-keyword">except</tt> <tt class="py-name">EnvironmentError</tt><tt class="py-op">:</tt> </tt>
<a name="L738"></a><tt class="py-lineno"> 738</tt>  <tt class="py-line">        <tt class="py-keyword">raise</tt> <tt class="py-name">EnvironmentError</tt><tt class="py-op">(</tt><tt class="py-string">"Scalable Vector Graphics (SVG) format requires the program 'pdf2svg'. "</tt> </tt>
<a name="L739"></a><tt class="py-lineno"> 739</tt>  <tt class="py-line">                                <tt class="py-string">"Cannot find 'pdf2svg' on search path."</tt><tt class="py-op">)</tt> </tt>
<a name="L740"></a><tt class="py-lineno"> 740</tt>  <tt class="py-line"> </tt>
<a name="L741"></a><tt class="py-lineno"> 741</tt>  <tt class="py-line">    <tt class="py-keyword">import</tt> <tt class="py-name">tempfile</tt><tt class="py-op">,</tt> <tt class="py-name">os</tt> </tt>
<a name="L742"></a><tt class="py-lineno"> 742</tt>  <tt class="py-line">    <tt class="py-name">fpdfi</tt><tt class="py-op">,</tt> <tt class="py-name">fname_pdf</tt> <tt class="py-op">=</tt> <tt class="py-name">tempfile</tt><tt class="py-op">.</tt><tt class="py-name">mkstemp</tt><tt class="py-op">(</tt><tt class="py-name">suffix</tt><tt class="py-op">=</tt><tt class="py-string">".pdf"</tt><tt class="py-op">)</tt> </tt>
<a name="L743"></a><tt class="py-lineno"> 743</tt>  <tt class="py-line">    <tt class="py-name">fsvgi</tt><tt class="py-op">,</tt> <tt class="py-name">fname_svg</tt> <tt class="py-op">=</tt> <tt class="py-name">tempfile</tt><tt class="py-op">.</tt><tt class="py-name">mkstemp</tt><tt class="py-op">(</tt><tt class="py-name">suffix</tt><tt class="py-op">=</tt><tt class="py-string">".svg"</tt><tt class="py-op">)</tt> </tt>
<a name="L744"></a><tt class="py-lineno"> 744</tt>  <tt class="py-line">    <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L745"></a><tt class="py-lineno"> 745</tt>  <tt class="py-line">         </tt>
<a name="L746"></a><tt class="py-lineno"> 746</tt>  <tt class="py-line">        <tt class="py-name">fpdf2</tt> <tt class="py-op">=</tt> <tt class="py-name">open</tt><tt class="py-op">(</tt><tt class="py-name">fname_pdf</tt><tt class="py-op">,</tt> <tt class="py-string">'w'</tt><tt class="py-op">)</tt> </tt>
<a name="L747"></a><tt class="py-lineno"> 747</tt>  <tt class="py-line">        <tt class="py-name">fpdf2</tt><tt class="py-op">.</tt><tt class="py-name">write</tt><tt class="py-op">(</tt><tt class="py-name">fpdf</tt><tt class="py-op">.</tt><tt class="py-name">getvalue</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">)</tt> </tt>
<a name="L748"></a><tt class="py-lineno"> 748</tt>  <tt class="py-line">        <tt class="py-name">fpdf2</tt><tt class="py-op">.</tt><tt class="py-name">seek</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">)</tt> </tt>
<a name="L749"></a><tt class="py-lineno"> 749</tt>  <tt class="py-line">   </tt>
<a name="L750"></a><tt class="py-lineno"> 750</tt>  <tt class="py-line">        <tt class="py-name">args</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">command</tt><tt class="py-op">,</tt> <tt class="py-name">fname_pdf</tt><tt class="py-op">,</tt> <tt class="py-name">fname_svg</tt><tt class="py-op">]</tt> </tt>
<a name="L751"></a><tt class="py-lineno"> 751</tt>  <tt class="py-line">        <tt class="py-name">p</tt> <tt class="py-op">=</tt> <tt class="py-name">Popen</tt><tt class="py-op">(</tt><tt class="py-name">args</tt><tt class="py-op">)</tt> </tt>
<a name="L752"></a><tt class="py-lineno"> 752</tt>  <tt class="py-line">        <tt class="py-op">(</tt><tt class="py-name">out</tt><tt class="py-op">,</tt><tt class="py-name">err</tt><tt class="py-op">)</tt> <tt class="py-op">=</tt> <tt class="py-name">p</tt><tt class="py-op">.</tt><tt class="py-name">communicate</tt><tt class="py-op">(</tt><tt class="py-op">)</tt>  </tt>
<a name="L753"></a><tt class="py-lineno"> 753</tt>  <tt class="py-line"> </tt>
<a name="L754"></a><tt class="py-lineno"> 754</tt>  <tt class="py-line">        <tt class="py-name">fsvg</tt> <tt class="py-op">=</tt> <tt class="py-name">open</tt><tt class="py-op">(</tt><tt class="py-name">fname_svg</tt><tt class="py-op">)</tt> </tt>
<a name="L755"></a><tt class="py-lineno"> 755</tt>  <tt class="py-line">        <tt class="py-name">fout</tt><tt class="py-op">.</tt><tt class="py-name">write</tt><tt class="py-op">(</tt><tt class="py-name">fsvg</tt><tt class="py-op">.</tt><tt class="py-name">read</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L756"></a><tt class="py-lineno"> 756</tt>  <tt class="py-line">    <tt class="py-keyword">finally</tt><tt class="py-op">:</tt> </tt>
<a name="L757"></a><tt class="py-lineno"> 757</tt>  <tt class="py-line">        <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">remove</tt><tt class="py-op">(</tt><tt class="py-name">fname_svg</tt><tt class="py-op">)</tt> </tt>
<a name="L758"></a><tt class="py-lineno"> 758</tt>  <tt class="py-line">        <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">remove</tt><tt class="py-op">(</tt><tt class="py-name">fname_pdf</tt><tt class="py-op">)</tt> </tt>
</div><a name="L759"></a><tt class="py-lineno"> 759</tt>  <tt class="py-line"> </tt>
<a name="png_formatter"></a><div id="png_formatter-def"><a name="L760"></a><tt class="py-lineno"> 760</tt>  <tt class="py-line"> </tt>
<a name="L761"></a><tt class="py-lineno"> 761</tt> <a class="py-toggle" href="#" id="png_formatter-toggle" onclick="return toggle('png_formatter');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="weblogolib-module.html#png_formatter">png_formatter</a><tt class="py-op">(</tt><tt class="py-param">data</tt><tt class="py-op">,</tt> <tt class="py-param">format</tt><tt class="py-op">,</tt> <tt class="py-param">fout</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt>  </tt>
</div><a name="L762"></a><tt class="py-lineno"> 762</tt>  <tt class="py-line">    <tt class="py-docstring">""" Generate a logo in PNG format."""</tt> </tt>
<a name="L763"></a><tt class="py-lineno"> 763</tt>  <tt class="py-line">    <tt class="py-name">_bitmap_formatter</tt><tt class="py-op">(</tt><tt class="py-name">data</tt><tt class="py-op">,</tt> <tt class="py-name">format</tt><tt class="py-op">,</tt> <tt class="py-name">fout</tt><tt class="py-op">,</tt> <tt class="py-name">device</tt><tt class="py-op">=</tt><tt class="py-string">"png"</tt><tt class="py-op">)</tt> </tt>
</div><a name="L764"></a><tt class="py-lineno"> 764</tt>  <tt class="py-line"> </tt>
<a name="png_print_formatter"></a><div id="png_print_formatter-def"><a name="L765"></a><tt class="py-lineno"> 765</tt>  <tt class="py-line"> </tt>
<a name="L766"></a><tt class="py-lineno"> 766</tt> <a class="py-toggle" href="#" id="png_print_formatter-toggle" onclick="return toggle('png_print_formatter');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="weblogolib-module.html#png_print_formatter">png_print_formatter</a><tt class="py-op">(</tt><tt class="py-param">data</tt><tt class="py-op">,</tt> <tt class="py-param">format</tt><tt class="py-op">,</tt> <tt class="py-param">fout</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt>  </tt>
</div><a name="L767"></a><tt class="py-lineno"> 767</tt>  <tt class="py-line">    <tt class="py-docstring">""" Generate a logo in PNG format with print quality (600 DPI) resolution."""</tt> </tt>
<a name="L768"></a><tt class="py-lineno"> 768</tt>  <tt class="py-line">    <tt class="py-name">format</tt><tt class="py-op">.</tt><tt class="py-name">resolution</tt> <tt class="py-op">=</tt> <tt class="py-number">600</tt> </tt>
<a name="L769"></a><tt class="py-lineno"> 769</tt>  <tt class="py-line">    <tt class="py-name">_bitmap_formatter</tt><tt class="py-op">(</tt><tt class="py-name">data</tt><tt class="py-op">,</tt> <tt class="py-name">format</tt><tt class="py-op">,</tt> <tt class="py-name">fout</tt><tt class="py-op">,</tt> <tt class="py-name">device</tt><tt class="py-op">=</tt><tt class="py-string">"png"</tt><tt class="py-op">)</tt> </tt>
</div><a name="L770"></a><tt class="py-lineno"> 770</tt>  <tt class="py-line"> </tt>
<a name="txt_formatter"></a><div id="txt_formatter-def"><a name="L771"></a><tt class="py-lineno"> 771</tt>  <tt class="py-line"> </tt>
<a name="L772"></a><tt class="py-lineno"> 772</tt> <a class="py-toggle" href="#" id="txt_formatter-toggle" onclick="return toggle('txt_formatter');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="weblogolib-module.html#txt_formatter">txt_formatter</a><tt class="py-op">(</tt> <tt class="py-param">logodata</tt><tt class="py-op">,</tt> <tt class="py-param">format</tt><tt class="py-op">,</tt> <tt class="py-param">fout</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
</div><div id="txt_formatter-collapsed" style="display:none;" pad="++++" indent="++++"></div><div id="txt_formatter-expanded"><a name="L773"></a><tt class="py-lineno"> 773</tt>  <tt class="py-line">    <tt class="py-docstring">""" Create a text representation of the logo data. </tt> </tt>
<a name="L774"></a><tt class="py-lineno"> 774</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L775"></a><tt class="py-lineno"> 775</tt>  <tt class="py-line">    <tt class="py-keyword">print</tt> <tt class="py-op">&gt;&gt;</tt><tt class="py-name">fout</tt><tt class="py-op">,</tt> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">logodata</tt><tt class="py-op">)</tt> </tt>
</div><a name="L776"></a><tt class="py-lineno"> 776</tt>  <tt class="py-line"> </tt>
<a name="eps_formatter"></a><div id="eps_formatter-def"><a name="L777"></a><tt class="py-lineno"> 777</tt>  <tt class="py-line">    </tt>
<a name="L778"></a><tt class="py-lineno"> 778</tt>  <tt class="py-line"> </tt>
<a name="L779"></a><tt class="py-lineno"> 779</tt>  <tt class="py-line">     </tt>
<a name="L780"></a><tt class="py-lineno"> 780</tt> <a class="py-toggle" href="#" id="eps_formatter-toggle" onclick="return toggle('eps_formatter');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="weblogolib-module.html#eps_formatter">eps_formatter</a><tt class="py-op">(</tt> <tt class="py-param">logodata</tt><tt class="py-op">,</tt> <tt class="py-param">format</tt><tt class="py-op">,</tt> <tt class="py-param">fout</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
</div><div id="eps_formatter-collapsed" style="display:none;" pad="++++" indent="++++"></div><div id="eps_formatter-expanded"><a name="L781"></a><tt class="py-lineno"> 781</tt>  <tt class="py-line">    <tt class="py-docstring">""" Generate a logo in Encapsulated Postscript (EPS)"""</tt> </tt>
<a name="L782"></a><tt class="py-lineno"> 782</tt>  <tt class="py-line">     </tt>
<a name="L783"></a><tt class="py-lineno"> 783</tt>  <tt class="py-line">    <tt class="py-name">substitutions</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L784"></a><tt class="py-lineno"> 784</tt>  <tt class="py-line">    <tt class="py-name">from_format</tt> <tt class="py-op">=</tt><tt class="py-op">[</tt> </tt>
<a name="L785"></a><tt class="py-lineno"> 785</tt>  <tt class="py-line">        <tt class="py-string">"creation_date"</tt><tt class="py-op">,</tt>    <tt class="py-string">"logo_width"</tt><tt class="py-op">,</tt>           <tt class="py-string">"logo_height"</tt><tt class="py-op">,</tt>       </tt>
<a name="L786"></a><tt class="py-lineno"> 786</tt>  <tt class="py-line">        <tt class="py-string">"lines_per_logo"</tt><tt class="py-op">,</tt>   <tt class="py-string">"line_width"</tt><tt class="py-op">,</tt>           <tt class="py-string">"line_height"</tt><tt class="py-op">,</tt> </tt>
<a name="L787"></a><tt class="py-lineno"> 787</tt>  <tt class="py-line">        <tt class="py-string">"line_margin_right"</tt><tt class="py-op">,</tt><tt class="py-string">"line_margin_left"</tt><tt class="py-op">,</tt>     <tt class="py-string">"line_margin_bottom"</tt><tt class="py-op">,</tt> </tt>
<a name="L788"></a><tt class="py-lineno"> 788</tt>  <tt class="py-line">        <tt class="py-string">"line_margin_top"</tt><tt class="py-op">,</tt>  <tt class="py-string">"title_height"</tt><tt class="py-op">,</tt>         <tt class="py-string">"xaxis_label_height"</tt><tt class="py-op">,</tt> </tt>
<a name="L789"></a><tt class="py-lineno"> 789</tt>  <tt class="py-line">        <tt class="py-string">"creator_text"</tt><tt class="py-op">,</tt>     <tt class="py-string">"logo_title"</tt><tt class="py-op">,</tt>           <tt class="py-string">"logo_margin"</tt><tt class="py-op">,</tt> </tt>
<a name="L790"></a><tt class="py-lineno"> 790</tt>  <tt class="py-line">        <tt class="py-string">"stroke_width"</tt><tt class="py-op">,</tt>     <tt class="py-string">"tic_length"</tt><tt class="py-op">,</tt>            </tt>
<a name="L791"></a><tt class="py-lineno"> 791</tt>  <tt class="py-line">        <tt class="py-string">"stacks_per_line"</tt><tt class="py-op">,</tt>  <tt class="py-string">"stack_margin"</tt><tt class="py-op">,</tt> </tt>
<a name="L792"></a><tt class="py-lineno"> 792</tt>  <tt class="py-line">        <tt class="py-string">"yaxis_label"</tt><tt class="py-op">,</tt>      <tt class="py-string">"yaxis_tic_interval"</tt><tt class="py-op">,</tt>   <tt class="py-string">"yaxis_minor_tic_interval"</tt><tt class="py-op">,</tt> </tt>
<a name="L793"></a><tt class="py-lineno"> 793</tt>  <tt class="py-line">        <tt class="py-string">"xaxis_label"</tt><tt class="py-op">,</tt>      <tt class="py-string">"xaxis_tic_interval"</tt><tt class="py-op">,</tt>   <tt class="py-string">"number_interval"</tt><tt class="py-op">,</tt> </tt>
<a name="L794"></a><tt class="py-lineno"> 794</tt>  <tt class="py-line">        <tt class="py-string">"fineprint"</tt><tt class="py-op">,</tt>        <tt class="py-string">"shrink_fraction"</tt><tt class="py-op">,</tt>      <tt class="py-string">"errorbar_fraction"</tt><tt class="py-op">,</tt> </tt>
<a name="L795"></a><tt class="py-lineno"> 795</tt>  <tt class="py-line">        <tt class="py-string">"errorbar_width_fraction"</tt><tt class="py-op">,</tt> </tt>
<a name="L796"></a><tt class="py-lineno"> 796</tt>  <tt class="py-line">        <tt class="py-string">"errorbar_gray"</tt><tt class="py-op">,</tt>    <tt class="py-string">"small_fontsize"</tt><tt class="py-op">,</tt>       <tt class="py-string">"fontsize"</tt><tt class="py-op">,</tt> </tt>
<a name="L797"></a><tt class="py-lineno"> 797</tt>  <tt class="py-line">        <tt class="py-string">"title_fontsize"</tt><tt class="py-op">,</tt>   <tt class="py-string">"number_fontsize"</tt><tt class="py-op">,</tt>      <tt class="py-string">"text_font"</tt><tt class="py-op">,</tt> </tt>
<a name="L798"></a><tt class="py-lineno"> 798</tt>  <tt class="py-line">        <tt class="py-string">"logo_font"</tt><tt class="py-op">,</tt>        <tt class="py-string">"title_font"</tt><tt class="py-op">,</tt>           </tt>
<a name="L799"></a><tt class="py-lineno"> 799</tt>  <tt class="py-line">        <tt class="py-string">"logo_label"</tt><tt class="py-op">,</tt>       <tt class="py-string">"yaxis_scale"</tt><tt class="py-op">,</tt>          <tt class="py-string">"end_type"</tt><tt class="py-op">,</tt> </tt>
<a name="L800"></a><tt class="py-lineno"> 800</tt>  <tt class="py-line">        <tt class="py-string">"debug"</tt><tt class="py-op">,</tt>            <tt class="py-string">"show_title"</tt><tt class="py-op">,</tt>           <tt class="py-string">"show_xaxis"</tt><tt class="py-op">,</tt> </tt>
<a name="L801"></a><tt class="py-lineno"> 801</tt>  <tt class="py-line">        <tt class="py-string">"show_xaxis_label"</tt><tt class="py-op">,</tt> <tt class="py-string">"show_yaxis"</tt><tt class="py-op">,</tt>           <tt class="py-string">"show_yaxis_label"</tt><tt class="py-op">,</tt> </tt>
<a name="L802"></a><tt class="py-lineno"> 802</tt>  <tt class="py-line">        <tt class="py-string">"show_boxes"</tt><tt class="py-op">,</tt>       <tt class="py-string">"show_errorbars"</tt><tt class="py-op">,</tt>       <tt class="py-string">"show_fineprint"</tt><tt class="py-op">,</tt> </tt>
<a name="L803"></a><tt class="py-lineno"> 803</tt>  <tt class="py-line">        <tt class="py-string">"rotate_numbers"</tt><tt class="py-op">,</tt>   <tt class="py-string">"show_ends"</tt><tt class="py-op">,</tt>            <tt class="py-string">"stack_height"</tt><tt class="py-op">,</tt> </tt>
<a name="L804"></a><tt class="py-lineno"> 804</tt>  <tt class="py-line">        <tt class="py-string">"stack_width"</tt> </tt>
<a name="L805"></a><tt class="py-lineno"> 805</tt>  <tt class="py-line">        <tt class="py-op">]</tt> </tt>
<a name="L806"></a><tt class="py-lineno"> 806</tt>  <tt class="py-line">    </tt>
<a name="L807"></a><tt class="py-lineno"> 807</tt>  <tt class="py-line">    <tt class="py-keyword">for</tt> <tt class="py-name">s</tt> <tt class="py-keyword">in</tt> <tt class="py-name">from_format</tt> <tt class="py-op">:</tt> </tt>
<a name="L808"></a><tt class="py-lineno"> 808</tt>  <tt class="py-line">        <tt class="py-name">substitutions</tt><tt class="py-op">[</tt><tt class="py-name">s</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">getattr</tt><tt class="py-op">(</tt><tt class="py-name">format</tt><tt class="py-op">,</tt><tt class="py-name">s</tt><tt class="py-op">)</tt> </tt>
<a name="L809"></a><tt class="py-lineno"> 809</tt>  <tt class="py-line"> </tt>
<a name="L810"></a><tt class="py-lineno"> 810</tt>  <tt class="py-line">    <tt class="py-name">substitutions</tt><tt class="py-op">[</tt><tt class="py-string">"shrink"</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">format</tt><tt class="py-op">.</tt><tt class="py-name">show_boxes</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">lower</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L811"></a><tt class="py-lineno"> 811</tt>  <tt class="py-line"> </tt>
<a name="L812"></a><tt class="py-lineno"> 812</tt>  <tt class="py-line"> </tt>
<a name="L813"></a><tt class="py-lineno"> 813</tt>  <tt class="py-line">    <tt class="py-comment"># --------- COLORS --------------</tt> </tt>
<a name="L814"></a><tt class="py-lineno"> 814</tt>  <tt class="py-line"><tt class="py-comment"></tt>    <tt class="py-keyword">def</tt> <tt class="py-def-name">format_color</tt><tt class="py-op">(</tt><tt class="py-param">color</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L815"></a><tt class="py-lineno"> 815</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt>  <tt class="py-string">" "</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt> <tt class="py-op">(</tt><tt class="py-string">"["</tt><tt class="py-op">,</tt><tt class="py-name">str</tt><tt class="py-op">(</tt><tt id="link-55" class="py-name"><a title="weblogolib.color
weblogolib.colorscheme.ColorScheme.color" class="py-name" href="#" onclick="return doclink('link-55', 'color', 'link-1');">color</a></tt><tt class="py-op">.</tt><tt class="py-name">red</tt><tt class="py-op">)</tt> <tt class="py-op">,</tt> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt id="link-56" class="py-name"><a title="weblogolib.color
weblogolib.colorscheme.ColorScheme.color" class="py-name" href="#" onclick="return doclink('link-56', 'color', 'link-1');">color</a></tt><tt class="py-op">.</tt><tt class="py-name">green</tt><tt class="py-op">)</tt><tt class="py-op">,</tt>  </tt>
<a name="L816"></a><tt class="py-lineno"> 816</tt>  <tt class="py-line">            <tt class="py-name">str</tt><tt class="py-op">(</tt><tt id="link-57" class="py-name"><a title="weblogolib.color
weblogolib.colorscheme.ColorScheme.color" class="py-name" href="#" onclick="return doclink('link-57', 'color', 'link-1');">color</a></tt><tt class="py-op">.</tt><tt class="py-name">blue</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-string">"]"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt>   </tt>
</div><a name="L817"></a><tt class="py-lineno"> 817</tt>  <tt class="py-line"> </tt>
<a name="L818"></a><tt class="py-lineno"> 818</tt>  <tt class="py-line">    <tt class="py-name">substitutions</tt><tt class="py-op">[</tt><tt class="py-string">"default_color"</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">format_color</tt><tt class="py-op">(</tt><tt class="py-name">format</tt><tt class="py-op">.</tt><tt class="py-name">default_color</tt><tt class="py-op">)</tt> </tt>
<a name="L819"></a><tt class="py-lineno"> 819</tt>  <tt class="py-line"> </tt>
<a name="L820"></a><tt class="py-lineno"> 820</tt>  <tt class="py-line">    <tt class="py-name">colors</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt>   </tt>
<a name="L821"></a><tt class="py-lineno"> 821</tt>  <tt class="py-line">    <tt class="py-keyword">for</tt> <tt class="py-name">group</tt> <tt class="py-keyword">in</tt> <tt class="py-name">format</tt><tt class="py-op">.</tt><tt class="py-name">color_scheme</tt><tt class="py-op">.</tt><tt class="py-name">groups</tt> <tt class="py-op">:</tt> </tt>
<a name="L822"></a><tt class="py-lineno"> 822</tt>  <tt class="py-line">        <tt class="py-name">cf</tt> <tt class="py-op">=</tt> <tt class="py-name">format_color</tt><tt class="py-op">(</tt><tt class="py-name">group</tt><tt class="py-op">.</tt><tt id="link-58" class="py-name"><a title="weblogolib.color
weblogolib.colorscheme.ColorScheme.color" class="py-name" href="#" onclick="return doclink('link-58', 'color', 'link-1');">color</a></tt><tt class="py-op">)</tt> </tt>
<a name="L823"></a><tt class="py-lineno"> 823</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt class="py-name">s</tt> <tt class="py-keyword">in</tt> <tt class="py-name">group</tt><tt class="py-op">.</tt><tt class="py-name">symbols</tt> <tt class="py-op">:</tt> </tt>
<a name="L824"></a><tt class="py-lineno"> 824</tt>  <tt class="py-line">            <tt class="py-name">colors</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt> <tt class="py-string">"  ("</tt><tt class="py-op">+</tt><tt class="py-name">s</tt><tt class="py-op">+</tt><tt class="py-string">") "</tt> <tt class="py-op">+</tt> <tt class="py-name">cf</tt> <tt class="py-op">)</tt> </tt>
<a name="L825"></a><tt class="py-lineno"> 825</tt>  <tt class="py-line">    <tt class="py-name">substitutions</tt><tt class="py-op">[</tt><tt class="py-string">"color_dict"</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-string">"\n"</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-name">colors</tt><tt class="py-op">)</tt> </tt>
<a name="L826"></a><tt class="py-lineno"> 826</tt>  <tt class="py-line">         </tt>
<a name="L827"></a><tt class="py-lineno"> 827</tt>  <tt class="py-line">    <tt class="py-name">data</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L828"></a><tt class="py-lineno"> 828</tt>  <tt class="py-line">     </tt>
<a name="L829"></a><tt class="py-lineno"> 829</tt>  <tt class="py-line">    <tt class="py-comment"># Unit conversion. 'None' for probability units</tt> </tt>
<a name="L830"></a><tt class="py-lineno"> 830</tt>  <tt class="py-line"><tt class="py-comment"></tt>    <tt class="py-name">conv_factor</tt> <tt class="py-op">=</tt> <tt id="link-59" class="py-name"><a title="weblogolib.std_units" class="py-name" href="#" onclick="return doclink('link-59', 'std_units', 'link-34');">std_units</a></tt><tt class="py-op">[</tt><tt class="py-name">format</tt><tt class="py-op">.</tt><tt class="py-name">unit_name</tt><tt class="py-op">]</tt> </tt>
<a name="L831"></a><tt class="py-lineno"> 831</tt>  <tt class="py-line">     </tt>
<a name="L832"></a><tt class="py-lineno"> 832</tt>  <tt class="py-line">    <tt class="py-name">data</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-string">"StartLine"</tt><tt class="py-op">)</tt> </tt>
<a name="L833"></a><tt class="py-lineno"> 833</tt>  <tt class="py-line">     </tt>
<a name="L834"></a><tt class="py-lineno"> 834</tt>  <tt class="py-line"> </tt>
<a name="L835"></a><tt class="py-lineno"> 835</tt>  <tt class="py-line">    <tt class="py-name">seq_from</tt> <tt class="py-op">=</tt> <tt class="py-name">format</tt><tt class="py-op">.</tt><tt class="py-name">logo_start</tt><tt class="py-op">-</tt> <tt class="py-name">format</tt><tt class="py-op">.</tt><tt class="py-name">first_index</tt> </tt>
<a name="L836"></a><tt class="py-lineno"> 836</tt>  <tt class="py-line">    <tt class="py-name">seq_to</tt> <tt class="py-op">=</tt> <tt class="py-name">format</tt><tt class="py-op">.</tt><tt class="py-name">logo_end</tt> <tt class="py-op">-</tt> <tt class="py-name">format</tt><tt class="py-op">.</tt><tt class="py-name">first_index</tt> <tt class="py-op">+</tt><tt class="py-number">1</tt> </tt>
<a name="L837"></a><tt class="py-lineno"> 837</tt>  <tt class="py-line"> </tt>
<a name="L838"></a><tt class="py-lineno"> 838</tt>  <tt class="py-line">    <tt class="py-comment"># seq_index : zero based index into sequence data</tt> </tt>
<a name="L839"></a><tt class="py-lineno"> 839</tt>  <tt class="py-line"><tt class="py-comment"></tt>    <tt class="py-comment"># logo_index : User visible coordinate, first_index based</tt> </tt>
<a name="L840"></a><tt class="py-lineno"> 840</tt>  <tt class="py-line"><tt class="py-comment"></tt>    <tt class="py-comment"># stack_index : zero based index of visible stacks</tt> </tt>
<a name="L841"></a><tt class="py-lineno"> 841</tt>  <tt class="py-line"><tt class="py-comment"></tt>    <tt class="py-keyword">for</tt> <tt class="py-name">seq_index</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">seq_from</tt><tt class="py-op">,</tt> <tt class="py-name">seq_to</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
<a name="L842"></a><tt class="py-lineno"> 842</tt>  <tt class="py-line">        <tt class="py-name">logo_index</tt> <tt class="py-op">=</tt> <tt class="py-name">seq_index</tt> <tt class="py-op">+</tt> <tt class="py-name">format</tt><tt class="py-op">.</tt><tt class="py-name">first_index</tt>  </tt>
<a name="L843"></a><tt class="py-lineno"> 843</tt>  <tt class="py-line">        <tt class="py-name">stack_index</tt> <tt class="py-op">=</tt> <tt class="py-name">seq_index</tt> <tt class="py-op">-</tt> <tt class="py-name">seq_from</tt> </tt>
<a name="L844"></a><tt class="py-lineno"> 844</tt>  <tt class="py-line">         </tt>
<a name="L845"></a><tt class="py-lineno"> 845</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">stack_index</tt><tt class="py-op">!=</tt><tt class="py-number">0</tt> <tt class="py-keyword">and</tt> <tt class="py-op">(</tt><tt class="py-name">stack_index</tt> <tt class="py-op">%</tt> <tt class="py-name">format</tt><tt class="py-op">.</tt><tt class="py-name">stacks_per_line</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt><tt class="py-number">0</tt> <tt class="py-op">:</tt> </tt>
<a name="L846"></a><tt class="py-lineno"> 846</tt>  <tt class="py-line">            <tt class="py-name">data</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-string">""</tt><tt class="py-op">)</tt> </tt>
<a name="L847"></a><tt class="py-lineno"> 847</tt>  <tt class="py-line">            <tt class="py-name">data</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-string">"EndLine"</tt><tt class="py-op">)</tt> </tt>
<a name="L848"></a><tt class="py-lineno"> 848</tt>  <tt class="py-line">            <tt class="py-name">data</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-string">"StartLine"</tt><tt class="py-op">)</tt> </tt>
<a name="L849"></a><tt class="py-lineno"> 849</tt>  <tt class="py-line">            <tt class="py-name">data</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-string">""</tt><tt class="py-op">)</tt> </tt>
<a name="L850"></a><tt class="py-lineno"> 850</tt>  <tt class="py-line">         </tt>
<a name="L851"></a><tt class="py-lineno"> 851</tt>  <tt class="py-line">        <tt class="py-name">data</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-string">"(%s) StartStack"</tt> <tt class="py-op">%</tt> <tt class="py-name">format</tt><tt class="py-op">.</tt><tt class="py-name">annotate</tt><tt class="py-op">[</tt><tt class="py-name">seq_index</tt><tt class="py-op">]</tt> <tt class="py-op">)</tt> </tt>
<a name="L852"></a><tt class="py-lineno"> 852</tt>  <tt class="py-line"> </tt>
<a name="L853"></a><tt class="py-lineno"> 853</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">conv_factor</tt><tt class="py-op">:</tt>  </tt>
<a name="L854"></a><tt class="py-lineno"> 854</tt>  <tt class="py-line">            <tt class="py-name">stack_height</tt> <tt class="py-op">=</tt> <tt class="py-name">logodata</tt><tt class="py-op">.</tt><tt class="py-name">entropy</tt><tt class="py-op">[</tt><tt class="py-name">seq_index</tt><tt class="py-op">]</tt> <tt class="py-op">*</tt> <tt id="link-60" class="py-name"><a title="weblogolib.std_units" class="py-name" href="#" onclick="return doclink('link-60', 'std_units', 'link-34');">std_units</a></tt><tt class="py-op">[</tt><tt class="py-name">format</tt><tt class="py-op">.</tt><tt class="py-name">unit_name</tt><tt class="py-op">]</tt> </tt>
<a name="L855"></a><tt class="py-lineno"> 855</tt>  <tt class="py-line">        <tt class="py-keyword">else</tt> <tt class="py-op">:</tt> </tt>
<a name="L856"></a><tt class="py-lineno"> 856</tt>  <tt class="py-line">            <tt class="py-name">stack_height</tt> <tt class="py-op">=</tt> <tt class="py-number">1.0</tt> <tt class="py-comment"># Probability</tt> </tt>
<a name="L857"></a><tt class="py-lineno"> 857</tt>  <tt class="py-line"> </tt>
<a name="L858"></a><tt class="py-lineno"> 858</tt>  <tt class="py-line">        <tt class="py-name">s</tt> <tt class="py-op">=</tt> <tt class="py-name">zip</tt><tt class="py-op">(</tt><tt class="py-name">logodata</tt><tt class="py-op">.</tt><tt class="py-name">counts</tt><tt class="py-op">[</tt><tt class="py-name">seq_index</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">logodata</tt><tt class="py-op">.</tt><tt class="py-name">alphabet</tt><tt class="py-op">)</tt> </tt>
<a name="L859"></a><tt class="py-lineno"> 859</tt>  <tt class="py-line">        <tt class="py-keyword">def</tt> <tt class="py-def-name">mycmp</tt><tt class="py-op">(</tt> <tt class="py-param">c1</tt><tt class="py-op">,</tt> <tt class="py-param">c2</tt> <tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
<a name="L860"></a><tt class="py-lineno"> 860</tt>  <tt class="py-line">            <tt class="py-comment"># Sort by frequency. If equal frequency then reverse alphabetic</tt> </tt>
<a name="L861"></a><tt class="py-lineno"> 861</tt>  <tt class="py-line"><tt class="py-comment"></tt>            <tt class="py-keyword">if</tt> <tt class="py-name">c1</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-name">c2</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-op">:</tt> <tt class="py-keyword">return</tt> <tt class="py-name">cmp</tt><tt class="py-op">(</tt><tt class="py-name">c2</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">c1</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L862"></a><tt class="py-lineno"> 862</tt>  <tt class="py-line">            <tt class="py-keyword">return</tt> <tt class="py-name">cmp</tt><tt class="py-op">(</tt><tt class="py-name">c1</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">c2</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
</div><a name="L863"></a><tt class="py-lineno"> 863</tt>  <tt class="py-line">         </tt>
<a name="L864"></a><tt class="py-lineno"> 864</tt>  <tt class="py-line">        <tt class="py-name">s</tt><tt class="py-op">.</tt><tt class="py-name">sort</tt><tt class="py-op">(</tt><tt class="py-name">mycmp</tt><tt class="py-op">)</tt> </tt>
<a name="L865"></a><tt class="py-lineno"> 865</tt>  <tt class="py-line"> </tt>
<a name="L866"></a><tt class="py-lineno"> 866</tt>  <tt class="py-line">        <tt class="py-name">C</tt> <tt class="py-op">=</tt> <tt class="py-name">float</tt><tt class="py-op">(</tt><tt class="py-name">sum</tt><tt class="py-op">(</tt><tt class="py-name">logodata</tt><tt class="py-op">.</tt><tt class="py-name">counts</tt><tt class="py-op">[</tt><tt class="py-name">seq_index</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">)</tt>  </tt>
<a name="L867"></a><tt class="py-lineno"> 867</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">C</tt> <tt class="py-op">&gt;</tt> <tt class="py-number">0.0</tt> <tt class="py-op">:</tt> </tt>
<a name="L868"></a><tt class="py-lineno"> 868</tt>  <tt class="py-line">            <tt class="py-name">fraction_width</tt> <tt class="py-op">=</tt> <tt class="py-number">1.0</tt> </tt>
<a name="L869"></a><tt class="py-lineno"> 869</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">format</tt><tt class="py-op">.</tt><tt class="py-name">scale_width</tt> <tt class="py-op">:</tt> </tt>
<a name="L870"></a><tt class="py-lineno"> 870</tt>  <tt class="py-line">                <tt class="py-name">fraction_width</tt> <tt class="py-op">=</tt> <tt class="py-name">logodata</tt><tt class="py-op">.</tt><tt class="py-name">weight</tt><tt class="py-op">[</tt><tt class="py-name">seq_index</tt><tt class="py-op">]</tt>  </tt>
<a name="L871"></a><tt class="py-lineno"> 871</tt>  <tt class="py-line">            <tt class="py-comment"># print &gt;&gt;sys.stderr, fraction_width</tt> </tt>
<a name="L872"></a><tt class="py-lineno"> 872</tt>  <tt class="py-line"><tt class="py-comment"></tt>            <tt class="py-keyword">for</tt> <tt class="py-name">c</tt> <tt class="py-keyword">in</tt> <tt class="py-name">s</tt><tt class="py-op">:</tt> </tt>
<a name="L873"></a><tt class="py-lineno"> 873</tt>  <tt class="py-line">                <tt class="py-name">data</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-string">" %f %f (%s) ShowSymbol"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">fraction_width</tt><tt class="py-op">,</tt> <tt class="py-name">c</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">*</tt><tt class="py-name">stack_height</tt><tt class="py-op">/</tt><tt class="py-name">C</tt><tt class="py-op">,</tt> <tt class="py-name">c</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> <tt class="py-op">)</tt> </tt>
<a name="L874"></a><tt class="py-lineno"> 874</tt>  <tt class="py-line"> </tt>
<a name="L875"></a><tt class="py-lineno"> 875</tt>  <tt class="py-line">        <tt class="py-comment"># Draw error bar on top of logo. Replaced by DrawErrorbarFirst above.</tt> </tt>
<a name="L876"></a><tt class="py-lineno"> 876</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-keyword">if</tt> <tt class="py-name">logodata</tt><tt class="py-op">.</tt><tt class="py-name">entropy_interval</tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</tt> <tt class="py-keyword">and</tt> <tt class="py-name">conv_factor</tt><tt class="py-op">:</tt> </tt>
<a name="L877"></a><tt class="py-lineno"> 877</tt>  <tt class="py-line">            <tt class="py-name">low</tt><tt class="py-op">,</tt> <tt class="py-name">high</tt> <tt class="py-op">=</tt> <tt class="py-name">logodata</tt><tt class="py-op">.</tt><tt class="py-name">entropy_interval</tt><tt class="py-op">[</tt><tt class="py-name">seq_index</tt><tt class="py-op">]</tt> </tt>
<a name="L878"></a><tt class="py-lineno"> 878</tt>  <tt class="py-line">            <tt class="py-name">center</tt> <tt class="py-op">=</tt> <tt class="py-name">logodata</tt><tt class="py-op">.</tt><tt class="py-name">entropy</tt><tt class="py-op">[</tt><tt class="py-name">seq_index</tt><tt class="py-op">]</tt> </tt>
<a name="L879"></a><tt class="py-lineno"> 879</tt>  <tt class="py-line"> </tt>
<a name="L880"></a><tt class="py-lineno"> 880</tt>  <tt class="py-line">            <tt class="py-name">down</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-name">center</tt> <tt class="py-op">-</tt> <tt class="py-name">low</tt><tt class="py-op">)</tt> <tt class="py-op">*</tt> <tt class="py-name">conv_factor</tt> </tt>
<a name="L881"></a><tt class="py-lineno"> 881</tt>  <tt class="py-line">            <tt class="py-name">up</tt>   <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-name">high</tt> <tt class="py-op">-</tt> <tt class="py-name">center</tt><tt class="py-op">)</tt> <tt class="py-op">*</tt> <tt class="py-name">conv_factor</tt> </tt>
<a name="L882"></a><tt class="py-lineno"> 882</tt>  <tt class="py-line">            <tt class="py-name">data</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-string">" %f %f DrawErrorbar"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">down</tt><tt class="py-op">,</tt> <tt class="py-name">up</tt><tt class="py-op">)</tt> <tt class="py-op">)</tt> </tt>
<a name="L883"></a><tt class="py-lineno"> 883</tt>  <tt class="py-line">             </tt>
<a name="L884"></a><tt class="py-lineno"> 884</tt>  <tt class="py-line">        <tt class="py-name">data</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-string">"EndStack"</tt><tt class="py-op">)</tt> </tt>
<a name="L885"></a><tt class="py-lineno"> 885</tt>  <tt class="py-line">        <tt class="py-name">data</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-string">""</tt><tt class="py-op">)</tt> </tt>
<a name="L886"></a><tt class="py-lineno"> 886</tt>  <tt class="py-line">                </tt>
<a name="L887"></a><tt class="py-lineno"> 887</tt>  <tt class="py-line">    <tt class="py-name">data</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-string">"EndLine"</tt><tt class="py-op">)</tt> </tt>
<a name="L888"></a><tt class="py-lineno"> 888</tt>  <tt class="py-line">    <tt class="py-name">substitutions</tt><tt class="py-op">[</tt><tt class="py-string">"logo_data"</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-string">"\n"</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-name">data</tt><tt class="py-op">)</tt>   </tt>
<a name="L889"></a><tt class="py-lineno"> 889</tt>  <tt class="py-line"> </tt>
<a name="L890"></a><tt class="py-lineno"> 890</tt>  <tt class="py-line"> </tt>
<a name="L891"></a><tt class="py-lineno"> 891</tt>  <tt class="py-line">    <tt class="py-comment"># Create and output logo</tt> </tt>
<a name="L892"></a><tt class="py-lineno"> 892</tt>  <tt class="py-line"><tt class="py-comment"></tt>    <tt class="py-name">template</tt> <tt class="py-op">=</tt> <tt id="link-61" class="py-name"><a title="weblogolib._cgi.resource_string" class="py-name" href="#" onclick="return doclink('link-61', 'resource_string', 'link-0');">resource_string</a></tt><tt class="py-op">(</tt> <tt class="py-name">__name__</tt><tt class="py-op">,</tt> <tt class="py-string">'template.eps'</tt><tt class="py-op">,</tt> <tt class="py-name">__file__</tt><tt class="py-op">)</tt> </tt>
<a name="L893"></a><tt class="py-lineno"> 893</tt>  <tt class="py-line">    <tt class="py-name">logo</tt> <tt class="py-op">=</tt> <tt class="py-name">Template</tt><tt class="py-op">(</tt><tt class="py-name">template</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">substitute</tt><tt class="py-op">(</tt><tt class="py-name">substitutions</tt><tt class="py-op">)</tt> </tt>
<a name="L894"></a><tt class="py-lineno"> 894</tt>  <tt class="py-line">    <tt class="py-keyword">print</tt> <tt class="py-op">&gt;&gt;</tt><tt class="py-name">fout</tt><tt class="py-op">,</tt> <tt class="py-name">logo</tt> </tt>
</div><a name="L895"></a><tt class="py-lineno"> 895</tt>  <tt class="py-line">  </tt>
<a name="L896"></a><tt class="py-lineno"> 896</tt>  <tt class="py-line"> </tt>
<a name="L897"></a><tt class="py-lineno"> 897</tt>  <tt class="py-line"><tt class="py-comment"># map between output format names and logo  </tt> </tt>
<a name="L898"></a><tt class="py-lineno"> 898</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt id="link-62" class="py-name" targets="Variable weblogolib.formatters=weblogolib-module.html#formatters"><a title="weblogolib.formatters" class="py-name" href="#" onclick="return doclink('link-62', 'formatters', 'link-62');">formatters</a></tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt> </tt>
<a name="L899"></a><tt class="py-lineno"> 899</tt>  <tt class="py-line">    <tt class="py-string">'eps'</tt><tt class="py-op">:</tt> <tt id="link-63" class="py-name"><a title="weblogolib.eps_formatter" class="py-name" href="#" onclick="return doclink('link-63', 'eps_formatter', 'link-48');">eps_formatter</a></tt><tt class="py-op">,</tt>  </tt>
<a name="L900"></a><tt class="py-lineno"> 900</tt>  <tt class="py-line">    <tt class="py-string">'pdf'</tt><tt class="py-op">:</tt> <tt id="link-64" class="py-name"><a title="weblogolib.pdf_formatter" class="py-name" href="#" onclick="return doclink('link-64', 'pdf_formatter', 'link-54');">pdf_formatter</a></tt><tt class="py-op">,</tt> </tt>
<a name="L901"></a><tt class="py-lineno"> 901</tt>  <tt class="py-line">    <tt class="py-string">'png'</tt><tt class="py-op">:</tt> <tt id="link-65" class="py-name" targets="Function weblogolib.png_formatter()=weblogolib-module.html#png_formatter"><a title="weblogolib.png_formatter" class="py-name" href="#" onclick="return doclink('link-65', 'png_formatter', 'link-65');">png_formatter</a></tt><tt class="py-op">,</tt> </tt>
<a name="L902"></a><tt class="py-lineno"> 902</tt>  <tt class="py-line">    <tt class="py-string">'png_print'</tt> <tt class="py-op">:</tt> <tt id="link-66" class="py-name" targets="Function weblogolib.png_print_formatter()=weblogolib-module.html#png_print_formatter"><a title="weblogolib.png_print_formatter" class="py-name" href="#" onclick="return doclink('link-66', 'png_print_formatter', 'link-66');">png_print_formatter</a></tt><tt class="py-op">,</tt> </tt>
<a name="L903"></a><tt class="py-lineno"> 903</tt>  <tt class="py-line">    <tt class="py-string">'jpeg'</tt>  <tt class="py-op">:</tt> <tt id="link-67" class="py-name" targets="Function weblogolib.jpeg_formatter()=weblogolib-module.html#jpeg_formatter"><a title="weblogolib.jpeg_formatter" class="py-name" href="#" onclick="return doclink('link-67', 'jpeg_formatter', 'link-67');">jpeg_formatter</a></tt><tt class="py-op">,</tt> </tt>
<a name="L904"></a><tt class="py-lineno"> 904</tt>  <tt class="py-line">    <tt class="py-string">'svg'</tt>   <tt class="py-op">:</tt> <tt class="py-name">svg_formatter</tt><tt class="py-op">,</tt> </tt>
<a name="L905"></a><tt class="py-lineno"> 905</tt>  <tt class="py-line">    <tt class="py-string">'logodata'</tt> <tt class="py-op">:</tt> <tt id="link-68" class="py-name" targets="Function weblogolib.txt_formatter()=weblogolib-module.html#txt_formatter"><a title="weblogolib.txt_formatter" class="py-name" href="#" onclick="return doclink('link-68', 'txt_formatter', 'link-68');">txt_formatter</a></tt><tt class="py-op">,</tt>           </tt>
<a name="L906"></a><tt class="py-lineno"> 906</tt>  <tt class="py-line">    <tt class="py-op">}</tt>      </tt>
<a name="L907"></a><tt class="py-lineno"> 907</tt>  <tt class="py-line">     </tt>
<a name="L908"></a><tt class="py-lineno"> 908</tt>  <tt class="py-line"><tt class="py-name">default_formatter</tt> <tt class="py-op">=</tt> <tt id="link-69" class="py-name"><a title="weblogolib.eps_formatter" class="py-name" href="#" onclick="return doclink('link-69', 'eps_formatter', 'link-48');">eps_formatter</a></tt> </tt>
<a name="parse_prior"></a><div id="parse_prior-def"><a name="L909"></a><tt class="py-lineno"> 909</tt>  <tt class="py-line"> </tt>
<a name="L910"></a><tt class="py-lineno"> 910</tt>  <tt class="py-line"> </tt>
<a name="L911"></a><tt class="py-lineno"> 911</tt>  <tt class="py-line"> </tt>
<a name="L912"></a><tt class="py-lineno"> 912</tt>  <tt class="py-line"> </tt>
<a name="L913"></a><tt class="py-lineno"> 913</tt>  <tt class="py-line"> </tt>
<a name="L914"></a><tt class="py-lineno"> 914</tt> <a class="py-toggle" href="#" id="parse_prior-toggle" onclick="return toggle('parse_prior');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="weblogolib-module.html#parse_prior">parse_prior</a><tt class="py-op">(</tt><tt class="py-param">composition</tt><tt class="py-op">,</tt> <tt class="py-param">alphabet</tt><tt class="py-op">,</tt> <tt class="py-param">weight</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
</div><div id="parse_prior-collapsed" style="display:none;" pad="++++" indent="++++"></div><div id="parse_prior-expanded"><a name="L915"></a><tt class="py-lineno"> 915</tt>  <tt class="py-line">    <tt class="py-docstring">""" Parse a description of the expected monomer distribution of a sequence.</tt> </tt>
<a name="L916"></a><tt class="py-lineno"> 916</tt>  <tt class="py-line"><tt class="py-docstring">    </tt> </tt>
<a name="L917"></a><tt class="py-lineno"> 917</tt>  <tt class="py-line"><tt class="py-docstring">    Valid compositions:</tt> </tt>
<a name="L918"></a><tt class="py-lineno"> 918</tt>  <tt class="py-line"><tt class="py-docstring">    </tt> </tt>
<a name="L919"></a><tt class="py-lineno"> 919</tt>  <tt class="py-line"><tt class="py-docstring">    - None or 'none' :      No composition sepecified </tt> </tt>
<a name="L920"></a><tt class="py-lineno"> 920</tt>  <tt class="py-line"><tt class="py-docstring">    - 'auto' or 'automatic': Use the typical average distribution</tt> </tt>
<a name="L921"></a><tt class="py-lineno"> 921</tt>  <tt class="py-line"><tt class="py-docstring">                            for proteins and an equiprobable distribution for</tt> </tt>
<a name="L922"></a><tt class="py-lineno"> 922</tt>  <tt class="py-line"><tt class="py-docstring">                            everything else.    </tt> </tt>
<a name="L923"></a><tt class="py-lineno"> 923</tt>  <tt class="py-line"><tt class="py-docstring">    - 'equiprobable' :      All monomers have the same probability.</tt> </tt>
<a name="L924"></a><tt class="py-lineno"> 924</tt>  <tt class="py-line"><tt class="py-docstring">    - a percentage, e.g. '45%' or a fraction '0.45':</tt> </tt>
<a name="L925"></a><tt class="py-lineno"> 925</tt>  <tt class="py-line"><tt class="py-docstring">                            The fraction of CG bases for nucleotide alphabets</tt> </tt>
<a name="L926"></a><tt class="py-lineno"> 926</tt>  <tt class="py-line"><tt class="py-docstring">    - a species name, e.g. 'E. coli', 'H. sapiens' :</tt> </tt>
<a name="L927"></a><tt class="py-lineno"> 927</tt>  <tt class="py-line"><tt class="py-docstring">                            Use the average CG percentage for the specie's      </tt> </tt>
<a name="L928"></a><tt class="py-lineno"> 928</tt>  <tt class="py-line"><tt class="py-docstring">                            genome.</tt> </tt>
<a name="L929"></a><tt class="py-lineno"> 929</tt>  <tt class="py-line"><tt class="py-docstring">    - An explicit distribution,  e.g. {'A':10, 'C':40, 'G':40, 'T':10}</tt> </tt>
<a name="L930"></a><tt class="py-lineno"> 930</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L931"></a><tt class="py-lineno"> 931</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt id="link-70" class="py-name" targets="Variable weblogolib._cgi.composition=weblogolib._cgi-module.html#composition"><a title="weblogolib._cgi.composition" class="py-name" href="#" onclick="return doclink('link-70', 'composition', 'link-70');">composition</a></tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> <tt class="py-keyword">return</tt> <tt class="py-name">None</tt> </tt>
<a name="L932"></a><tt class="py-lineno"> 932</tt>  <tt class="py-line">    <tt class="py-name">comp</tt> <tt class="py-op">=</tt> <tt id="link-71" class="py-name"><a title="weblogolib._cgi.composition" class="py-name" href="#" onclick="return doclink('link-71', 'composition', 'link-70');">composition</a></tt><tt class="py-op">.</tt><tt class="py-name">strip</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L933"></a><tt class="py-lineno"> 933</tt>  <tt class="py-line">     </tt>
<a name="L934"></a><tt class="py-lineno"> 934</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">comp</tt><tt class="py-op">.</tt><tt class="py-name">lower</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-string">'none'</tt><tt class="py-op">:</tt> <tt class="py-keyword">return</tt> <tt class="py-name">None</tt> </tt>
<a name="L935"></a><tt class="py-lineno"> 935</tt>  <tt class="py-line">     </tt>
<a name="L936"></a><tt class="py-lineno"> 936</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">weight</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt> <tt class="py-keyword">and</tt> <tt class="py-name">alphabet</tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> <tt class="py-name">weight</tt> <tt class="py-op">=</tt> <tt class="py-name">float</tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">alphabet</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L937"></a><tt class="py-lineno"> 937</tt>  <tt class="py-line">     </tt>
<a name="L938"></a><tt class="py-lineno"> 938</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">comp</tt><tt class="py-op">.</tt><tt class="py-name">lower</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-string">'equiprobable'</tt> <tt class="py-op">:</tt> </tt>
<a name="L939"></a><tt class="py-lineno"> 939</tt>  <tt class="py-line">        <tt class="py-name">prior</tt> <tt class="py-op">=</tt> <tt class="py-name">weight</tt> <tt class="py-op">*</tt> <tt id="link-72" class="py-name" targets="Function weblogolib.equiprobable_distribution()=weblogolib-module.html#equiprobable_distribution"><a title="weblogolib.equiprobable_distribution" class="py-name" href="#" onclick="return doclink('link-72', 'equiprobable_distribution', 'link-72');">equiprobable_distribution</a></tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">alphabet</tt><tt class="py-op">)</tt><tt class="py-op">)</tt>  </tt>
<a name="L940"></a><tt class="py-lineno"> 940</tt>  <tt class="py-line">    <tt class="py-keyword">elif</tt> <tt class="py-name">comp</tt><tt class="py-op">.</tt><tt class="py-name">lower</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-string">'auto'</tt> <tt class="py-keyword">or</tt> <tt class="py-name">comp</tt><tt class="py-op">.</tt><tt class="py-name">lower</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-string">'automatic'</tt><tt class="py-op">:</tt> </tt>
<a name="L941"></a><tt class="py-lineno"> 941</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">alphabet</tt> <tt class="py-op">==</tt> <tt class="py-name">unambiguous_protein_alphabet</tt> <tt class="py-op">:</tt> </tt>
<a name="L942"></a><tt class="py-lineno"> 942</tt>  <tt class="py-line">            <tt class="py-name">prior</tt> <tt class="py-op">=</tt>  <tt class="py-name">weight</tt> <tt class="py-op">*</tt> <tt class="py-name">asarray</tt><tt class="py-op">(</tt><tt id="link-73" class="py-name"><a title="weblogolib.aa_composition" class="py-name" href="#" onclick="return doclink('link-73', 'aa_composition', 'link-16');">aa_composition</a></tt><tt class="py-op">,</tt> <tt class="py-name">float64</tt><tt class="py-op">)</tt> </tt>
<a name="L943"></a><tt class="py-lineno"> 943</tt>  <tt class="py-line">        <tt class="py-keyword">else</tt> <tt class="py-op">:</tt> </tt>
<a name="L944"></a><tt class="py-lineno"> 944</tt>  <tt class="py-line">            <tt class="py-name">prior</tt> <tt class="py-op">=</tt> <tt class="py-name">weight</tt> <tt class="py-op">*</tt> <tt id="link-74" class="py-name"><a title="weblogolib.equiprobable_distribution" class="py-name" href="#" onclick="return doclink('link-74', 'equiprobable_distribution', 'link-72');">equiprobable_distribution</a></tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">alphabet</tt><tt class="py-op">)</tt><tt class="py-op">)</tt>  </tt>
<a name="L945"></a><tt class="py-lineno"> 945</tt>  <tt class="py-line">     </tt>
<a name="L946"></a><tt class="py-lineno"> 946</tt>  <tt class="py-line">    <tt class="py-keyword">elif</tt> <tt class="py-name">comp</tt> <tt class="py-keyword">in</tt> <tt id="link-75" class="py-name"><a title="weblogolib.std_percentCG" class="py-name" href="#" onclick="return doclink('link-75', 'std_percentCG', 'link-37');">std_percentCG</a></tt> <tt class="py-op">:</tt> </tt>
<a name="L947"></a><tt class="py-lineno"> 947</tt>  <tt class="py-line">        <tt class="py-name">prior</tt> <tt class="py-op">=</tt> <tt class="py-name">weight</tt> <tt class="py-op">*</tt> <tt id="link-76" class="py-name" targets="Function weblogolib.base_distribution()=weblogolib-module.html#base_distribution"><a title="weblogolib.base_distribution" class="py-name" href="#" onclick="return doclink('link-76', 'base_distribution', 'link-76');">base_distribution</a></tt><tt class="py-op">(</tt><tt id="link-77" class="py-name"><a title="weblogolib.std_percentCG" class="py-name" href="#" onclick="return doclink('link-77', 'std_percentCG', 'link-37');">std_percentCG</a></tt><tt class="py-op">[</tt><tt class="py-name">comp</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L948"></a><tt class="py-lineno"> 948</tt>  <tt class="py-line"> </tt>
<a name="L949"></a><tt class="py-lineno"> 949</tt>  <tt class="py-line">    <tt class="py-keyword">elif</tt> <tt class="py-name">comp</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-string">'%'</tt> <tt class="py-op">:</tt> </tt>
<a name="L950"></a><tt class="py-lineno"> 950</tt>  <tt class="py-line">        <tt class="py-name">prior</tt> <tt class="py-op">=</tt> <tt class="py-name">weight</tt> <tt class="py-op">*</tt> <tt id="link-78" class="py-name"><a title="weblogolib.base_distribution" class="py-name" href="#" onclick="return doclink('link-78', 'base_distribution', 'link-76');">base_distribution</a></tt><tt class="py-op">(</tt> <tt class="py-name">float</tt><tt class="py-op">(</tt><tt class="py-name">comp</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L951"></a><tt class="py-lineno"> 951</tt>  <tt class="py-line"> </tt>
<a name="L952"></a><tt class="py-lineno"> 952</tt>  <tt class="py-line">    <tt class="py-keyword">elif</tt> <tt class="py-name">isfloat</tt><tt class="py-op">(</tt><tt class="py-name">comp</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
<a name="L953"></a><tt class="py-lineno"> 953</tt>  <tt class="py-line">        <tt class="py-name">prior</tt> <tt class="py-op">=</tt> <tt class="py-name">weight</tt> <tt class="py-op">*</tt> <tt id="link-79" class="py-name"><a title="weblogolib.base_distribution" class="py-name" href="#" onclick="return doclink('link-79', 'base_distribution', 'link-76');">base_distribution</a></tt><tt class="py-op">(</tt> <tt class="py-name">float</tt><tt class="py-op">(</tt><tt class="py-name">comp</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-number">100.</tt> <tt class="py-op">)</tt> </tt>
<a name="L954"></a><tt class="py-lineno"> 954</tt>  <tt class="py-line"> </tt>
<a name="L955"></a><tt class="py-lineno"> 955</tt>  <tt class="py-line">    <tt class="py-keyword">elif</tt> <tt id="link-80" class="py-name"><a title="weblogolib._cgi.composition" class="py-name" href="#" onclick="return doclink('link-80', 'composition', 'link-70');">composition</a></tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-string">'{'</tt> <tt class="py-keyword">and</tt> <tt id="link-81" class="py-name"><a title="weblogolib._cgi.composition" class="py-name" href="#" onclick="return doclink('link-81', 'composition', 'link-70');">composition</a></tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-string">'}'</tt> <tt class="py-op">:</tt>  </tt>
<a name="L956"></a><tt class="py-lineno"> 956</tt>  <tt class="py-line">        <tt class="py-name">explicit</tt> <tt class="py-op">=</tt> <tt id="link-82" class="py-name"><a title="weblogolib._cgi.composition" class="py-name" href="#" onclick="return doclink('link-82', 'composition', 'link-70');">composition</a></tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">:</tt> <tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L957"></a><tt class="py-lineno"> 957</tt>  <tt class="py-line">        <tt class="py-name">explicit</tt> <tt class="py-op">=</tt> <tt class="py-name">explicit</tt><tt class="py-op">.</tt><tt class="py-name">replace</tt><tt class="py-op">(</tt><tt class="py-string">','</tt><tt class="py-op">,</tt><tt class="py-string">' '</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">replace</tt><tt class="py-op">(</tt><tt class="py-string">"'"</tt><tt class="py-op">,</tt> <tt class="py-string">' '</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">replace</tt><tt class="py-op">(</tt><tt class="py-string">'"'</tt><tt class="py-op">,</tt><tt class="py-string">' '</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">replace</tt><tt class="py-op">(</tt><tt class="py-string">':'</tt><tt class="py-op">,</tt> <tt class="py-string">' '</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">split</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L958"></a><tt class="py-lineno"> 958</tt>  <tt class="py-line">         </tt>
<a name="L959"></a><tt class="py-lineno"> 959</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">explicit</tt><tt class="py-op">)</tt> <tt class="py-op">!=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">alphabet</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-number">2</tt> <tt class="py-op">:</tt> </tt>
<a name="L960"></a><tt class="py-lineno"> 960</tt>  <tt class="py-line">            <tt class="py-comment">#print explicit</tt> </tt>
<a name="L961"></a><tt class="py-lineno"> 961</tt>  <tt class="py-line"><tt class="py-comment"></tt>            <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">(</tt><tt class="py-string">"Explicit prior does not match length of alphabet"</tt><tt class="py-op">)</tt> </tt>
<a name="L962"></a><tt class="py-lineno"> 962</tt>  <tt class="py-line">        <tt class="py-name">prior</tt> <tt class="py-op">=</tt> <tt class="py-op">-</tt> <tt class="py-name">ones</tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">alphabet</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">float64</tt><tt class="py-op">)</tt>  </tt>
<a name="L963"></a><tt class="py-lineno"> 963</tt>  <tt class="py-line">        <tt class="py-keyword">try</tt> <tt class="py-op">:</tt> </tt>
<a name="L964"></a><tt class="py-lineno"> 964</tt>  <tt class="py-line">            <tt class="py-keyword">for</tt> <tt class="py-name">r</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">explicit</tt><tt class="py-op">)</tt><tt class="py-op">/</tt><tt class="py-number">2</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
<a name="L965"></a><tt class="py-lineno"> 965</tt>  <tt class="py-line">                <tt class="py-name">letter</tt> <tt class="py-op">=</tt> <tt class="py-name">explicit</tt><tt class="py-op">[</tt><tt class="py-name">r</tt><tt class="py-op">*</tt><tt class="py-number">2</tt><tt class="py-op">]</tt> </tt>
<a name="L966"></a><tt class="py-lineno"> 966</tt>  <tt class="py-line">                <tt class="py-name">index</tt> <tt class="py-op">=</tt> <tt class="py-name">alphabet</tt><tt class="py-op">.</tt><tt class="py-name">ord</tt><tt class="py-op">(</tt><tt class="py-name">letter</tt><tt class="py-op">)</tt> </tt>
<a name="L967"></a><tt class="py-lineno"> 967</tt>  <tt class="py-line">                <tt class="py-name">value</tt> <tt class="py-op">=</tt> <tt class="py-name">float</tt><tt class="py-op">(</tt><tt class="py-name">explicit</tt><tt class="py-op">[</tt><tt class="py-name">r</tt><tt class="py-op">*</tt><tt class="py-number">2</tt> <tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L968"></a><tt class="py-lineno"> 968</tt>  <tt class="py-line">                <tt class="py-name">prior</tt><tt class="py-op">[</tt><tt class="py-name">index</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">value</tt> </tt>
<a name="L969"></a><tt class="py-lineno"> 969</tt>  <tt class="py-line">        <tt class="py-keyword">except</tt> <tt class="py-name">ValueError</tt> <tt class="py-op">:</tt> </tt>
<a name="L970"></a><tt class="py-lineno"> 970</tt>  <tt class="py-line">            <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">(</tt><tt class="py-string">"Cannot parse explicit composition"</tt><tt class="py-op">)</tt> </tt>
<a name="L971"></a><tt class="py-lineno"> 971</tt>  <tt class="py-line">     </tt>
<a name="L972"></a><tt class="py-lineno"> 972</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">any</tt><tt class="py-op">(</tt><tt class="py-name">prior</tt><tt class="py-op">==</tt><tt class="py-op">-</tt><tt class="py-number">1.</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
<a name="L973"></a><tt class="py-lineno"> 973</tt>  <tt class="py-line">            <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">(</tt><tt class="py-string">"Explicit prior does not match alphabet"</tt><tt class="py-op">)</tt>  </tt>
<a name="L974"></a><tt class="py-lineno"> 974</tt>  <tt class="py-line">        <tt class="py-name">prior</tt><tt class="py-op">/=</tt> <tt class="py-name">sum</tt><tt class="py-op">(</tt><tt class="py-name">prior</tt><tt class="py-op">)</tt> </tt>
<a name="L975"></a><tt class="py-lineno"> 975</tt>  <tt class="py-line">        <tt class="py-name">prior</tt> <tt class="py-op">*=</tt> <tt class="py-name">weight</tt> </tt>
<a name="L976"></a><tt class="py-lineno"> 976</tt>  <tt class="py-line">         </tt>
<a name="L977"></a><tt class="py-lineno"> 977</tt>  <tt class="py-line">         </tt>
<a name="L978"></a><tt class="py-lineno"> 978</tt>  <tt class="py-line">    <tt class="py-keyword">else</tt> <tt class="py-op">:</tt>  </tt>
<a name="L979"></a><tt class="py-lineno"> 979</tt>  <tt class="py-line">        <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">(</tt><tt class="py-string">"Unknown or malformed composition: %s"</tt><tt class="py-op">%</tt><tt id="link-83" class="py-name"><a title="weblogolib._cgi.composition" class="py-name" href="#" onclick="return doclink('link-83', 'composition', 'link-70');">composition</a></tt><tt class="py-op">)</tt> </tt>
<a name="L980"></a><tt class="py-lineno"> 980</tt>  <tt class="py-line">     </tt>
<a name="L981"></a><tt class="py-lineno"> 981</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">prior</tt><tt class="py-op">)</tt> <tt class="py-op">!=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">alphabet</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
<a name="L982"></a><tt class="py-lineno"> 982</tt>  <tt class="py-line">        <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">(</tt> </tt>
<a name="L983"></a><tt class="py-lineno"> 983</tt>  <tt class="py-line">            <tt class="py-string">"The sequence alphabet and composition are incompatible."</tt><tt class="py-op">)</tt> </tt>
<a name="L984"></a><tt class="py-lineno"> 984</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt class="py-name">prior</tt> </tt>
</div><a name="L985"></a><tt class="py-lineno"> 985</tt>  <tt class="py-line"> </tt>
<a name="base_distribution"></a><div id="base_distribution-def"><a name="L986"></a><tt class="py-lineno"> 986</tt>  <tt class="py-line">     </tt>
<a name="L987"></a><tt class="py-lineno"> 987</tt> <a class="py-toggle" href="#" id="base_distribution-toggle" onclick="return toggle('base_distribution');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="weblogolib-module.html#base_distribution">base_distribution</a><tt class="py-op">(</tt><tt class="py-param">percentCG</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
</div><div id="base_distribution-collapsed" style="display:none;" pad="++++" indent="++++"></div><div id="base_distribution-expanded"><a name="L988"></a><tt class="py-lineno"> 988</tt>  <tt class="py-line">    <tt class="py-name">A</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-number">1.</tt> <tt class="py-op">-</tt> <tt class="py-op">(</tt><tt class="py-name">percentCG</tt><tt class="py-op">/</tt><tt class="py-number">100.</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">/</tt><tt class="py-number">2.</tt> </tt>
<a name="L989"></a><tt class="py-lineno"> 989</tt>  <tt class="py-line">    <tt class="py-name">C</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-name">percentCG</tt><tt class="py-op">/</tt><tt class="py-number">100.</tt><tt class="py-op">)</tt><tt class="py-op">/</tt><tt class="py-number">2.</tt> </tt>
<a name="L990"></a><tt class="py-lineno"> 990</tt>  <tt class="py-line">    <tt class="py-name">G</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-name">percentCG</tt><tt class="py-op">/</tt><tt class="py-number">100.</tt><tt class="py-op">)</tt><tt class="py-op">/</tt><tt class="py-number">2.</tt> </tt>
<a name="L991"></a><tt class="py-lineno"> 991</tt>  <tt class="py-line">    <tt class="py-name">T</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-number">1.</tt> <tt class="py-op">-</tt> <tt class="py-op">(</tt><tt class="py-name">percentCG</tt><tt class="py-op">/</tt><tt class="py-number">100</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">/</tt><tt class="py-number">2.</tt> </tt>
<a name="L992"></a><tt class="py-lineno"> 992</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt class="py-name">asarray</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">A</tt><tt class="py-op">,</tt><tt class="py-name">C</tt><tt class="py-op">,</tt><tt class="py-name">G</tt><tt class="py-op">,</tt><tt class="py-name">T</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">float64</tt><tt class="py-op">)</tt>    </tt>
</div><a name="L993"></a><tt class="py-lineno"> 993</tt>  <tt class="py-line"> </tt>
<a name="equiprobable_distribution"></a><div id="equiprobable_distribution-def"><a name="L994"></a><tt class="py-lineno"> 994</tt> <a class="py-toggle" href="#" id="equiprobable_distribution-toggle" onclick="return toggle('equiprobable_distribution');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="weblogolib-module.html#equiprobable_distribution">equiprobable_distribution</a><tt class="py-op">(</tt> <tt class="py-param">length</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
</div><div id="equiprobable_distribution-collapsed" style="display:none;" pad="++++" indent="++++"></div><div id="equiprobable_distribution-expanded"><a name="L995"></a><tt class="py-lineno"> 995</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt class="py-name">ones</tt><tt class="py-op">(</tt> <tt class="py-op">(</tt><tt class="py-name">length</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">float64</tt><tt class="py-op">)</tt> <tt class="py-op">/</tt><tt class="py-name">length</tt>    </tt>
</div><a name="L996"></a><tt class="py-lineno"> 996</tt>  <tt class="py-line">   </tt>
<a name="read_seq_data"></a><div id="read_seq_data-def"><a name="L997"></a><tt class="py-lineno"> 997</tt>  <tt class="py-line"> </tt>
<a name="L998"></a><tt class="py-lineno"> 998</tt> <a class="py-toggle" href="#" id="read_seq_data-toggle" onclick="return toggle('read_seq_data');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="weblogolib-module.html#read_seq_data">read_seq_data</a><tt class="py-op">(</tt><tt class="py-param">fin</tt><tt class="py-op">,</tt>  </tt>
<a name="L999"></a><tt class="py-lineno"> 999</tt>  <tt class="py-line">                <tt class="py-param">input_parser</tt><tt class="py-op">=</tt><tt class="py-name">seq_io</tt><tt class="py-op">.</tt><tt class="py-name">read</tt><tt class="py-op">,</tt>  </tt>
<a name="L1000"></a><tt class="py-lineno">1000</tt>  <tt class="py-line">                <tt class="py-param">alphabet</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt>  </tt>
<a name="L1001"></a><tt class="py-lineno">1001</tt>  <tt class="py-line">                <tt class="py-param">ignore_lower_case</tt><tt class="py-op">=</tt><tt class="py-name">False</tt><tt class="py-op">,</tt>  </tt>
<a name="L1002"></a><tt class="py-lineno">1002</tt>  <tt class="py-line">                <tt class="py-param">max_file_size</tt><tt class="py-op">=</tt><tt class="py-number">0</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="read_seq_data-collapsed" style="display:none;" pad="++++" indent="++++"></div><div id="read_seq_data-expanded"><a name="L1003"></a><tt class="py-lineno">1003</tt>  <tt class="py-line">    <tt class="py-docstring">""" Read sequence data from the input stream and return a seqs object. </tt> </tt>
<a name="L1004"></a><tt class="py-lineno">1004</tt>  <tt class="py-line"><tt class="py-docstring">    </tt> </tt>
<a name="L1005"></a><tt class="py-lineno">1005</tt>  <tt class="py-line"><tt class="py-docstring">    The environment variable WEBLOGO_MAX_FILE_SIZE overides the max_file_size argument.</tt> </tt>
<a name="L1006"></a><tt class="py-lineno">1006</tt>  <tt class="py-line"><tt class="py-docstring">    Used to limit the load on the WebLogo webserver.</tt> </tt>
<a name="L1007"></a><tt class="py-lineno">1007</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L1008"></a><tt class="py-lineno">1008</tt>  <tt class="py-line"> </tt>
<a name="L1009"></a><tt class="py-lineno">1009</tt>  <tt class="py-line">    <tt class="py-name">max_file_size</tt> <tt class="py-op">=</tt><tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">environ</tt><tt class="py-op">.</tt><tt class="py-name">get</tt><tt class="py-op">(</tt><tt class="py-string">"WEBLOGO_MAX_FILE_SIZE"</tt><tt class="py-op">,</tt> <tt class="py-name">max_file_size</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L1010"></a><tt class="py-lineno">1010</tt>  <tt class="py-line"> </tt>
<a name="L1011"></a><tt class="py-lineno">1011</tt>  <tt class="py-line">    <tt class="py-comment"># If max_file_size is set, or if fin==stdin (which is non-seekable), we</tt> </tt>
<a name="L1012"></a><tt class="py-lineno">1012</tt>  <tt class="py-line"><tt class="py-comment"></tt>    <tt class="py-comment"># read the data and replace fin with a StringIO object. </tt> </tt>
<a name="L1013"></a><tt class="py-lineno">1013</tt>  <tt class="py-line"><tt class="py-comment"></tt>    <tt class="py-keyword">if</tt><tt class="py-op">(</tt><tt class="py-name">max_file_size</tt><tt class="py-op">&gt;</tt><tt class="py-number">0</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
<a name="L1014"></a><tt class="py-lineno">1014</tt>  <tt class="py-line">        <tt class="py-name">data</tt> <tt class="py-op">=</tt> <tt class="py-name">fin</tt><tt class="py-op">.</tt><tt class="py-name">read</tt><tt class="py-op">(</tt><tt class="py-name">max_file_size</tt><tt class="py-op">)</tt> </tt>
<a name="L1015"></a><tt class="py-lineno">1015</tt>  <tt class="py-line">        <tt class="py-name">more_data</tt> <tt class="py-op">=</tt> <tt class="py-name">fin</tt><tt class="py-op">.</tt><tt class="py-name">read</tt><tt class="py-op">(</tt><tt class="py-number">2</tt><tt class="py-op">)</tt> </tt>
<a name="L1016"></a><tt class="py-lineno">1016</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">more_data</tt> <tt class="py-op">!=</tt> <tt class="py-string">""</tt> <tt class="py-op">:</tt> </tt>
<a name="L1017"></a><tt class="py-lineno">1017</tt>  <tt class="py-line">            <tt class="py-keyword">raise</tt> <tt class="py-name">IOError</tt><tt class="py-op">(</tt><tt class="py-string">"File exceeds maximum allowed size: %d bytes"</tt>  <tt class="py-op">%</tt> <tt class="py-name">max_file_size</tt><tt class="py-op">)</tt>  </tt>
<a name="L1018"></a><tt class="py-lineno">1018</tt>  <tt class="py-line">        <tt class="py-name">fin</tt> <tt class="py-op">=</tt> <tt class="py-name">StringIO</tt><tt class="py-op">(</tt><tt class="py-name">data</tt><tt class="py-op">)</tt> </tt>
<a name="L1019"></a><tt class="py-lineno">1019</tt>  <tt class="py-line">    <tt class="py-keyword">elif</tt> <tt class="py-name">fin</tt> <tt class="py-op">==</tt> <tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">stdin</tt><tt class="py-op">:</tt> </tt>
<a name="L1020"></a><tt class="py-lineno">1020</tt>  <tt class="py-line">        <tt class="py-name">fin</tt> <tt class="py-op">=</tt> <tt class="py-name">StringIO</tt><tt class="py-op">(</tt><tt class="py-name">fin</tt><tt class="py-op">.</tt><tt class="py-name">read</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L1021"></a><tt class="py-lineno">1021</tt>  <tt class="py-line">         </tt>
<a name="L1022"></a><tt class="py-lineno">1022</tt>  <tt class="py-line">    <tt class="py-name">seqs</tt> <tt class="py-op">=</tt> <tt class="py-name">input_parser</tt><tt class="py-op">(</tt><tt class="py-name">fin</tt><tt class="py-op">)</tt> </tt>
<a name="L1023"></a><tt class="py-lineno">1023</tt>  <tt class="py-line"> </tt>
<a name="L1024"></a><tt class="py-lineno">1024</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">seqs</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt> <tt class="py-keyword">or</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">seqs</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt><tt class="py-number">0</tt> <tt class="py-op">:</tt> </tt>
<a name="L1025"></a><tt class="py-lineno">1025</tt>  <tt class="py-line">        <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">(</tt><tt class="py-string">"Please provide a multiple sequence alignment"</tt><tt class="py-op">)</tt> </tt>
<a name="L1026"></a><tt class="py-lineno">1026</tt>  <tt class="py-line">     </tt>
<a name="L1027"></a><tt class="py-lineno">1027</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">ignore_lower_case</tt> <tt class="py-op">:</tt> </tt>
<a name="L1028"></a><tt class="py-lineno">1028</tt>  <tt class="py-line">        <tt class="py-comment"># Case is significant. Do not count lower case letters.</tt> </tt>
<a name="L1029"></a><tt class="py-lineno">1029</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-keyword">for</tt> <tt class="py-name">i</tt><tt class="py-op">,</tt><tt class="py-name">s</tt> <tt class="py-keyword">in</tt> <tt class="py-name">enumerate</tt><tt class="py-op">(</tt><tt class="py-name">seqs</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
<a name="L1030"></a><tt class="py-lineno">1030</tt>  <tt class="py-line">            <tt class="py-name">seqs</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">s</tt><tt class="py-op">.</tt><tt class="py-name">mask</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L1031"></a><tt class="py-lineno">1031</tt>  <tt class="py-line"> </tt>
<a name="L1032"></a><tt class="py-lineno">1032</tt>  <tt class="py-line">    <tt class="py-comment"># Add alphabet to seqs.</tt> </tt>
<a name="L1033"></a><tt class="py-lineno">1033</tt>  <tt class="py-line"><tt class="py-comment"></tt>    <tt class="py-keyword">if</tt> <tt class="py-name">alphabet</tt> <tt class="py-op">:</tt> </tt>
<a name="L1034"></a><tt class="py-lineno">1034</tt>  <tt class="py-line">        <tt class="py-name">seqs</tt><tt class="py-op">.</tt><tt class="py-name">alphabet</tt> <tt class="py-op">=</tt> <tt class="py-name">Alphabet</tt><tt class="py-op">(</tt><tt class="py-name">alphabet</tt><tt class="py-op">)</tt>  </tt>
<a name="L1035"></a><tt class="py-lineno">1035</tt>  <tt class="py-line">    <tt class="py-keyword">else</tt> <tt class="py-op">:</tt> </tt>
<a name="L1036"></a><tt class="py-lineno">1036</tt>  <tt class="py-line">        <tt class="py-name">seqs</tt><tt class="py-op">.</tt><tt class="py-name">alphabet</tt> <tt class="py-op">=</tt> <tt class="py-name">Alphabet</tt><tt class="py-op">.</tt><tt class="py-name">which</tt><tt class="py-op">(</tt><tt class="py-name">seqs</tt><tt class="py-op">)</tt> </tt>
<a name="L1037"></a><tt class="py-lineno">1037</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt class="py-name">seqs</tt> </tt>
</div><a name="L1038"></a><tt class="py-lineno">1038</tt>  <tt class="py-line"> </tt>
<a name="LogoData"></a><div id="LogoData-def"><a name="L1039"></a><tt class="py-lineno">1039</tt>  <tt class="py-line"> </tt>
<a name="L1040"></a><tt class="py-lineno">1040</tt>  <tt class="py-line">     </tt>
<a name="L1041"></a><tt class="py-lineno">1041</tt> <a class="py-toggle" href="#" id="LogoData-toggle" onclick="return toggle('LogoData');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="weblogolib.LogoData-class.html">LogoData</a><tt class="py-op">(</tt><tt class="py-base-class">object</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
</div><div id="LogoData-collapsed" style="display:none;" pad="++++" indent="++++"></div><div id="LogoData-expanded"><a name="L1042"></a><tt class="py-lineno">1042</tt>  <tt class="py-line">    <tt class="py-docstring">"""The data needed to generate a sequence logo.</tt> </tt>
<a name="L1043"></a><tt class="py-lineno">1043</tt>  <tt class="py-line"><tt class="py-docstring">       </tt> </tt>
<a name="L1044"></a><tt class="py-lineno">1044</tt>  <tt class="py-line"><tt class="py-docstring">    - alphabet </tt> </tt>
<a name="L1045"></a><tt class="py-lineno">1045</tt>  <tt class="py-line"><tt class="py-docstring">    - length</tt> </tt>
<a name="L1046"></a><tt class="py-lineno">1046</tt>  <tt class="py-line"><tt class="py-docstring">    - counts  -- An array of character counts</tt> </tt>
<a name="L1047"></a><tt class="py-lineno">1047</tt>  <tt class="py-line"><tt class="py-docstring">    - entropy -- The relative entropy of each column</tt> </tt>
<a name="L1048"></a><tt class="py-lineno">1048</tt>  <tt class="py-line"><tt class="py-docstring">    - entropy_interval -- entropy confidence interval</tt> </tt>
<a name="L1049"></a><tt class="py-lineno">1049</tt>  <tt class="py-line"><tt class="py-docstring">     """</tt> </tt>
<a name="L1050"></a><tt class="py-lineno">1050</tt>  <tt class="py-line">      </tt>
<a name="LogoData.__init__"></a><div id="LogoData.__init__-def"><a name="L1051"></a><tt class="py-lineno">1051</tt> <a class="py-toggle" href="#" id="LogoData.__init__-toggle" onclick="return toggle('LogoData.__init__');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="weblogolib.LogoData-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">length</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">alphabet</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">counts</tt> <tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt>  </tt>
<a name="L1052"></a><tt class="py-lineno">1052</tt>  <tt class="py-line">            <tt class="py-param">entropy</tt> <tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">entropy_interval</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">weight</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
</div><div id="LogoData.__init__-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="LogoData.__init__-expanded"><a name="L1053"></a><tt class="py-lineno">1053</tt>  <tt class="py-line">        <tt class="py-docstring">"""Creates a new LogoData object"""</tt> </tt>
<a name="L1054"></a><tt class="py-lineno">1054</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">length</tt> <tt class="py-op">=</tt> <tt class="py-name">length</tt> </tt>
<a name="L1055"></a><tt class="py-lineno">1055</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">alphabet</tt> <tt class="py-op">=</tt> <tt class="py-name">alphabet</tt> </tt>
<a name="L1056"></a><tt class="py-lineno">1056</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">counts</tt> <tt class="py-op">=</tt> <tt class="py-name">counts</tt> </tt>
<a name="L1057"></a><tt class="py-lineno">1057</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">entropy</tt> <tt class="py-op">=</tt> <tt class="py-name">entropy</tt> </tt>
<a name="L1058"></a><tt class="py-lineno">1058</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">entropy_interval</tt> <tt class="py-op">=</tt> <tt class="py-name">entropy_interval</tt> </tt>
<a name="L1059"></a><tt class="py-lineno">1059</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">weight</tt> <tt class="py-op">=</tt> <tt class="py-name">weight</tt> </tt>
</div><a name="L1060"></a><tt class="py-lineno">1060</tt>  <tt class="py-line">         </tt>
<a name="L1061"></a><tt class="py-lineno">1061</tt>  <tt class="py-line"> </tt>
<a name="L1062"></a><tt class="py-lineno">1062</tt>  <tt class="py-line">    <tt class="py-decorator">@</tt><tt class="py-decorator">classmethod</tt>     </tt>
<a name="LogoData.from_counts"></a><div id="LogoData.from_counts-def"><a name="L1063"></a><tt class="py-lineno">1063</tt> <a class="py-toggle" href="#" id="LogoData.from_counts-toggle" onclick="return toggle('LogoData.from_counts');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="weblogolib.LogoData-class.html#from_counts">from_counts</a><tt class="py-op">(</tt><tt class="py-param">cls</tt><tt class="py-op">,</tt> <tt class="py-param">alphabet</tt><tt class="py-op">,</tt> <tt class="py-param">counts</tt><tt class="py-op">,</tt> <tt class="py-param">prior</tt><tt class="py-op">=</tt> <tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="LogoData.from_counts-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="LogoData.from_counts-expanded"><a name="L1064"></a><tt class="py-lineno">1064</tt>  <tt class="py-line">        <tt class="py-docstring">"""Build a LogoData object from counts."""</tt> </tt>
<a name="L1065"></a><tt class="py-lineno">1065</tt>  <tt class="py-line">        <tt class="py-comment"># Counts is a Motif object?</tt> </tt>
<a name="L1066"></a><tt class="py-lineno">1066</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-comment">#counts = counts.array</tt> </tt>
<a name="L1067"></a><tt class="py-lineno">1067</tt>  <tt class="py-line"><tt class="py-comment"></tt>         </tt>
<a name="L1068"></a><tt class="py-lineno">1068</tt>  <tt class="py-line">        <tt class="py-name">seq_length</tt><tt class="py-op">,</tt> <tt class="py-name">A</tt> <tt class="py-op">=</tt> <tt class="py-name">counts</tt><tt class="py-op">.</tt><tt class="py-name">shape</tt> </tt>
<a name="L1069"></a><tt class="py-lineno">1069</tt>  <tt class="py-line">         </tt>
<a name="L1070"></a><tt class="py-lineno">1070</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">prior</tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> <tt class="py-name">prior</tt> <tt class="py-op">=</tt> <tt class="py-name">array</tt><tt class="py-op">(</tt><tt class="py-name">prior</tt><tt class="py-op">,</tt> <tt class="py-name">float64</tt><tt class="py-op">)</tt> </tt>
<a name="L1071"></a><tt class="py-lineno">1071</tt>  <tt class="py-line">         </tt>
<a name="L1072"></a><tt class="py-lineno">1072</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">prior</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt> <tt class="py-op">:</tt> </tt>
<a name="L1073"></a><tt class="py-lineno">1073</tt>  <tt class="py-line">            <tt class="py-name">R</tt> <tt class="py-op">=</tt> <tt class="py-name">log</tt><tt class="py-op">(</tt><tt class="py-name">A</tt><tt class="py-op">)</tt> </tt>
<a name="L1074"></a><tt class="py-lineno">1074</tt>  <tt class="py-line">            <tt class="py-name">ent</tt> <tt class="py-op">=</tt> <tt class="py-name">zeros</tt><tt class="py-op">(</tt>  <tt class="py-name">seq_length</tt><tt class="py-op">,</tt> <tt class="py-name">float64</tt><tt class="py-op">)</tt> </tt>
<a name="L1075"></a><tt class="py-lineno">1075</tt>  <tt class="py-line">            <tt class="py-name">entropy_interval</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt>     </tt>
<a name="L1076"></a><tt class="py-lineno">1076</tt>  <tt class="py-line">            <tt class="py-keyword">for</tt> <tt class="py-name">i</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt> <tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-name">seq_length</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
<a name="L1077"></a><tt class="py-lineno">1077</tt>  <tt class="py-line">                <tt class="py-name">C</tt> <tt class="py-op">=</tt> <tt class="py-name">sum</tt><tt class="py-op">(</tt><tt class="py-name">counts</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">)</tt>  </tt>
<a name="L1078"></a><tt class="py-lineno">1078</tt>  <tt class="py-line">                <tt class="py-comment">#FIXME: fixup corebio.moremath.entropy()?</tt> </tt>
<a name="L1079"></a><tt class="py-lineno">1079</tt>  <tt class="py-line"><tt class="py-comment"></tt>                <tt class="py-keyword">if</tt> <tt class="py-name">C</tt> <tt class="py-op">==</tt> <tt class="py-number">0</tt> <tt class="py-op">:</tt> </tt>
<a name="L1080"></a><tt class="py-lineno">1080</tt>  <tt class="py-line">                    <tt class="py-name">ent</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-number">0.0</tt> </tt>
<a name="L1081"></a><tt class="py-lineno">1081</tt>  <tt class="py-line">                <tt class="py-keyword">else</tt> <tt class="py-op">:</tt> </tt>
<a name="L1082"></a><tt class="py-lineno">1082</tt>  <tt class="py-line">                    <tt class="py-name">ent</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">R</tt> <tt class="py-op">-</tt> <tt class="py-name">entropy</tt><tt class="py-op">(</tt><tt class="py-name">counts</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L1083"></a><tt class="py-lineno">1083</tt>  <tt class="py-line">        <tt class="py-keyword">else</tt> <tt class="py-op">:</tt> </tt>
<a name="L1084"></a><tt class="py-lineno">1084</tt>  <tt class="py-line">            <tt class="py-name">ent</tt> <tt class="py-op">=</tt> <tt class="py-name">zeros</tt><tt class="py-op">(</tt>  <tt class="py-name">seq_length</tt><tt class="py-op">,</tt> <tt class="py-name">float64</tt><tt class="py-op">)</tt> </tt>
<a name="L1085"></a><tt class="py-lineno">1085</tt>  <tt class="py-line">            <tt class="py-name">entropy_interval</tt> <tt class="py-op">=</tt> <tt class="py-name">zeros</tt><tt class="py-op">(</tt> <tt class="py-op">(</tt><tt class="py-name">seq_length</tt><tt class="py-op">,</tt><tt class="py-number">2</tt><tt class="py-op">)</tt> <tt class="py-op">,</tt> <tt class="py-name">float64</tt><tt class="py-op">)</tt> </tt>
<a name="L1086"></a><tt class="py-lineno">1086</tt>  <tt class="py-line">         </tt>
<a name="L1087"></a><tt class="py-lineno">1087</tt>  <tt class="py-line">            <tt class="py-name">R</tt> <tt class="py-op">=</tt> <tt class="py-name">log</tt><tt class="py-op">(</tt><tt class="py-name">A</tt><tt class="py-op">)</tt> </tt>
<a name="L1088"></a><tt class="py-lineno">1088</tt>  <tt class="py-line">             </tt>
<a name="L1089"></a><tt class="py-lineno">1089</tt>  <tt class="py-line">            <tt class="py-keyword">for</tt> <tt class="py-name">i</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt> <tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-name">seq_length</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
<a name="L1090"></a><tt class="py-lineno">1090</tt>  <tt class="py-line">                <tt class="py-name">alpha</tt> <tt class="py-op">=</tt> <tt class="py-name">array</tt><tt class="py-op">(</tt><tt class="py-name">counts</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt> <tt class="py-op">,</tt> <tt class="py-name">float64</tt><tt class="py-op">)</tt> </tt>
<a name="L1091"></a><tt class="py-lineno">1091</tt>  <tt class="py-line">                <tt class="py-name">alpha</tt> <tt class="py-op">+=</tt> <tt class="py-name">prior</tt> </tt>
<a name="L1092"></a><tt class="py-lineno">1092</tt>  <tt class="py-line">                 </tt>
<a name="L1093"></a><tt class="py-lineno">1093</tt>  <tt class="py-line">                <tt class="py-name">posterior</tt> <tt class="py-op">=</tt> <tt id="link-84" class="py-name"><a title="weblogolib.logomath.Dirichlet" class="py-name" href="#" onclick="return doclink('link-84', 'Dirichlet', 'link-4');">Dirichlet</a></tt><tt class="py-op">(</tt><tt class="py-name">alpha</tt><tt class="py-op">)</tt> </tt>
<a name="L1094"></a><tt class="py-lineno">1094</tt>  <tt class="py-line">                <tt class="py-name">ent</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">posterior</tt><tt class="py-op">.</tt><tt id="link-85" class="py-name" targets="Method weblogolib.logomath.Dirichlet.mean_relative_entropy()=weblogolib.logomath.Dirichlet-class.html#mean_relative_entropy"><a title="weblogolib.logomath.Dirichlet.mean_relative_entropy" class="py-name" href="#" onclick="return doclink('link-85', 'mean_relative_entropy', 'link-85');">mean_relative_entropy</a></tt><tt class="py-op">(</tt><tt class="py-name">prior</tt><tt class="py-op">/</tt><tt class="py-name">sum</tt><tt class="py-op">(</tt><tt class="py-name">prior</tt><tt class="py-op">)</tt><tt class="py-op">)</tt>  </tt>
<a name="L1095"></a><tt class="py-lineno">1095</tt>  <tt class="py-line">                <tt class="py-name">entropy_interval</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">entropy_interval</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> \ </tt>
<a name="L1096"></a><tt class="py-lineno">1096</tt>  <tt class="py-line">                    <tt class="py-name">posterior</tt><tt class="py-op">.</tt><tt id="link-86" class="py-name" targets="Method weblogolib.logomath.Dirichlet.interval_relative_entropy()=weblogolib.logomath.Dirichlet-class.html#interval_relative_entropy"><a title="weblogolib.logomath.Dirichlet.interval_relative_entropy" class="py-name" href="#" onclick="return doclink('link-86', 'interval_relative_entropy', 'link-86');">interval_relative_entropy</a></tt><tt class="py-op">(</tt><tt class="py-name">prior</tt><tt class="py-op">/</tt><tt class="py-name">sum</tt><tt class="py-op">(</tt><tt class="py-name">prior</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-number">0.95</tt><tt class="py-op">)</tt>  </tt>
<a name="L1097"></a><tt class="py-lineno">1097</tt>  <tt class="py-line">  </tt>
<a name="L1098"></a><tt class="py-lineno">1098</tt>  <tt class="py-line">        <tt class="py-name">weight</tt> <tt class="py-op">=</tt> <tt class="py-name">array</tt><tt class="py-op">(</tt> <tt class="py-name">na</tt><tt class="py-op">.</tt><tt class="py-name">sum</tt><tt class="py-op">(</tt><tt class="py-name">counts</tt><tt class="py-op">,</tt><tt class="py-name">axis</tt><tt class="py-op">=</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> <tt class="py-op">,</tt> <tt class="py-name">float</tt><tt class="py-op">)</tt>  </tt>
<a name="L1099"></a><tt class="py-lineno">1099</tt>  <tt class="py-line">        <tt class="py-name">weight</tt> <tt class="py-op">/=</tt> <tt class="py-name">max</tt><tt class="py-op">(</tt><tt class="py-name">weight</tt><tt class="py-op">)</tt> </tt>
<a name="L1100"></a><tt class="py-lineno">1100</tt>  <tt class="py-line">  </tt>
<a name="L1101"></a><tt class="py-lineno">1101</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">cls</tt><tt class="py-op">(</tt><tt class="py-name">seq_length</tt><tt class="py-op">,</tt> <tt class="py-name">alphabet</tt><tt class="py-op">,</tt> <tt class="py-name">counts</tt><tt class="py-op">,</tt> <tt class="py-name">ent</tt><tt class="py-op">,</tt> <tt class="py-name">entropy_interval</tt><tt class="py-op">,</tt> <tt class="py-name">weight</tt><tt class="py-op">)</tt> </tt>
</div><a name="L1102"></a><tt class="py-lineno">1102</tt>  <tt class="py-line"> </tt>
<a name="L1103"></a><tt class="py-lineno">1103</tt>  <tt class="py-line"> </tt>
<a name="L1104"></a><tt class="py-lineno">1104</tt>  <tt class="py-line">    <tt class="py-decorator">@</tt><tt class="py-decorator">classmethod</tt>     </tt>
<a name="LogoData.from_seqs"></a><div id="LogoData.from_seqs-def"><a name="L1105"></a><tt class="py-lineno">1105</tt> <a class="py-toggle" href="#" id="LogoData.from_seqs-toggle" onclick="return toggle('LogoData.from_seqs');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="weblogolib.LogoData-class.html#from_seqs">from_seqs</a><tt class="py-op">(</tt><tt class="py-param">cls</tt><tt class="py-op">,</tt> <tt class="py-param">seqs</tt><tt class="py-op">,</tt> <tt class="py-param">prior</tt><tt class="py-op">=</tt> <tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="LogoData.from_seqs-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="LogoData.from_seqs-expanded"><a name="L1106"></a><tt class="py-lineno">1106</tt>  <tt class="py-line">        <tt class="py-docstring">"""Build a LogoData object from a SeqList, a list of sequences."""</tt> </tt>
<a name="L1107"></a><tt class="py-lineno">1107</tt>  <tt class="py-line">        <tt class="py-comment"># --- VALIDATE DATA ---</tt> </tt>
<a name="L1108"></a><tt class="py-lineno">1108</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-comment"># check that at least one sequence of length at least 1 long</tt> </tt>
<a name="L1109"></a><tt class="py-lineno">1109</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">seqs</tt><tt class="py-op">)</tt><tt class="py-op">==</tt><tt class="py-number">0</tt> <tt class="py-keyword">or</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">seqs</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt><tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L1110"></a><tt class="py-lineno">1110</tt>  <tt class="py-line">            <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">(</tt><tt class="py-string">"No sequence data found."</tt><tt class="py-op">)</tt>    </tt>
<a name="L1111"></a><tt class="py-lineno">1111</tt>  <tt class="py-line">     </tt>
<a name="L1112"></a><tt class="py-lineno">1112</tt>  <tt class="py-line">        <tt class="py-comment"># Check sequence lengths    </tt> </tt>
<a name="L1113"></a><tt class="py-lineno">1113</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-name">seq_length</tt> <tt class="py-op">=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">seqs</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L1114"></a><tt class="py-lineno">1114</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt class="py-name">i</tt><tt class="py-op">,</tt><tt class="py-name">s</tt> <tt class="py-keyword">in</tt> <tt class="py-name">enumerate</tt><tt class="py-op">(</tt><tt class="py-name">seqs</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
<a name="L1115"></a><tt class="py-lineno">1115</tt>  <tt class="py-line">            <tt class="py-comment">#print i,s, len(s)</tt> </tt>
<a name="L1116"></a><tt class="py-lineno">1116</tt>  <tt class="py-line"><tt class="py-comment"></tt>            <tt class="py-comment">#TODO: Redundant? Should be checked in SeqList?</tt> </tt>
<a name="L1117"></a><tt class="py-lineno">1117</tt>  <tt class="py-line"><tt class="py-comment"></tt>            <tt class="py-keyword">if</tt> <tt class="py-name">seq_length</tt> <tt class="py-op">!=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">s</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
<a name="L1118"></a><tt class="py-lineno">1118</tt>  <tt class="py-line">                <tt class="py-keyword">raise</tt> <tt class="py-name">ArgumentError</tt><tt class="py-op">(</tt> </tt>
<a name="L1119"></a><tt class="py-lineno">1119</tt>  <tt class="py-line">    <tt class="py-string">"Sequence number %d differs in length from the previous sequences"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">i</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> <tt class="py-op">,</tt> </tt>
<a name="L1120"></a><tt class="py-lineno">1120</tt>  <tt class="py-line">                        <tt class="py-string">'sequences'</tt><tt class="py-op">)</tt> </tt>
<a name="L1121"></a><tt class="py-lineno">1121</tt>  <tt class="py-line"> </tt>
<a name="L1122"></a><tt class="py-lineno">1122</tt>  <tt class="py-line">        <tt class="py-comment"># FIXME: Check seqs.alphabet?</tt> </tt>
<a name="L1123"></a><tt class="py-lineno">1123</tt>  <tt class="py-line"><tt class="py-comment"></tt>         </tt>
<a name="L1124"></a><tt class="py-lineno">1124</tt>  <tt class="py-line">        <tt class="py-name">counts</tt> <tt class="py-op">=</tt> <tt class="py-name">seqs</tt><tt class="py-op">.</tt><tt class="py-name">profile</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L1125"></a><tt class="py-lineno">1125</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">cls</tt><tt class="py-op">.</tt><tt id="link-87" class="py-name" targets="Class Method weblogolib.LogoData.from_counts()=weblogolib.LogoData-class.html#from_counts"><a title="weblogolib.LogoData.from_counts" class="py-name" href="#" onclick="return doclink('link-87', 'from_counts', 'link-87');">from_counts</a></tt><tt class="py-op">(</tt><tt class="py-name">seqs</tt><tt class="py-op">.</tt><tt class="py-name">alphabet</tt><tt class="py-op">,</tt> <tt class="py-name">counts</tt><tt class="py-op">,</tt> <tt class="py-name">prior</tt><tt class="py-op">)</tt> </tt>
</div><a name="L1126"></a><tt class="py-lineno">1126</tt>  <tt class="py-line"> </tt>
<a name="L1127"></a><tt class="py-lineno">1127</tt>  <tt class="py-line"> </tt>
<a name="LogoData.__str__"></a><div id="LogoData.__str__-def"><a name="L1128"></a><tt class="py-lineno">1128</tt> <a class="py-toggle" href="#" id="LogoData.__str__-toggle" onclick="return toggle('LogoData.__str__');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="weblogolib.LogoData-class.html#__str__">__str__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
</div><div id="LogoData.__str__-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="LogoData.__str__-expanded"><a name="L1129"></a><tt class="py-lineno">1129</tt>  <tt class="py-line">        <tt class="py-name">out</tt> <tt class="py-op">=</tt> <tt class="py-name">StringIO</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L1130"></a><tt class="py-lineno">1130</tt>  <tt class="py-line">        <tt class="py-keyword">print</tt> <tt class="py-op">&gt;&gt;</tt><tt class="py-name">out</tt><tt class="py-op">,</tt> <tt class="py-string">'## LogoData'</tt> </tt>
<a name="L1131"></a><tt class="py-lineno">1131</tt>  <tt class="py-line">        <tt class="py-keyword">print</tt> <tt class="py-op">&gt;&gt;</tt><tt class="py-name">out</tt><tt class="py-op">,</tt> <tt class="py-string">'# First column is position number, counting from zero'</tt> </tt>
<a name="L1132"></a><tt class="py-lineno">1132</tt>  <tt class="py-line">        <tt class="py-keyword">print</tt> <tt class="py-op">&gt;&gt;</tt><tt class="py-name">out</tt><tt class="py-op">,</tt> <tt class="py-string">'# Subsequent columns are raw symbol counts'</tt> </tt>
<a name="L1133"></a><tt class="py-lineno">1133</tt>  <tt class="py-line">        <tt class="py-keyword">print</tt> <tt class="py-op">&gt;&gt;</tt><tt class="py-name">out</tt><tt class="py-op">,</tt> <tt class="py-string">'# Entropy is mean entropy measured in nats.'</tt>  </tt>
<a name="L1134"></a><tt class="py-lineno">1134</tt>  <tt class="py-line">        <tt class="py-keyword">print</tt> <tt class="py-op">&gt;&gt;</tt><tt class="py-name">out</tt><tt class="py-op">,</tt> <tt class="py-string">'# Low and High are the 95% confidence limits.'</tt> </tt>
<a name="L1135"></a><tt class="py-lineno">1135</tt>  <tt class="py-line">        <tt class="py-keyword">print</tt> <tt class="py-op">&gt;&gt;</tt><tt class="py-name">out</tt><tt class="py-op">,</tt> <tt class="py-string">'# Weight is the fraction of non-gap symbols in the column.'</tt> </tt>
<a name="L1136"></a><tt class="py-lineno">1136</tt>  <tt class="py-line">        <tt class="py-keyword">print</tt> <tt class="py-op">&gt;&gt;</tt><tt class="py-name">out</tt><tt class="py-op">,</tt> <tt class="py-string">'#\t'</tt> </tt>
<a name="L1137"></a><tt class="py-lineno">1137</tt>  <tt class="py-line">        <tt class="py-keyword">print</tt> <tt class="py-op">&gt;&gt;</tt><tt class="py-name">out</tt><tt class="py-op">,</tt> <tt class="py-string">'#\t'</tt><tt class="py-op">,</tt> </tt>
<a name="L1138"></a><tt class="py-lineno">1138</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt class="py-name">a</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">alphabet</tt> <tt class="py-op">:</tt> </tt>
<a name="L1139"></a><tt class="py-lineno">1139</tt>  <tt class="py-line">            <tt class="py-keyword">print</tt> <tt class="py-op">&gt;&gt;</tt><tt class="py-name">out</tt><tt class="py-op">,</tt> <tt class="py-name">a</tt><tt class="py-op">,</tt> <tt class="py-string">'\t'</tt><tt class="py-op">,</tt> </tt>
<a name="L1140"></a><tt class="py-lineno">1140</tt>  <tt class="py-line">        <tt class="py-keyword">print</tt> <tt class="py-op">&gt;&gt;</tt><tt class="py-name">out</tt><tt class="py-op">,</tt> <tt class="py-string">'Entropy\tLow\tHigh\tWeight'</tt> </tt>
<a name="L1141"></a><tt class="py-lineno">1141</tt>  <tt class="py-line">         </tt>
<a name="L1142"></a><tt class="py-lineno">1142</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt class="py-name">i</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">length</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
<a name="L1143"></a><tt class="py-lineno">1143</tt>  <tt class="py-line">            <tt class="py-keyword">print</tt> <tt class="py-op">&gt;&gt;</tt><tt class="py-name">out</tt><tt class="py-op">,</tt> <tt class="py-name">i</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-string">'\t'</tt><tt class="py-op">,</tt> </tt>
<a name="L1144"></a><tt class="py-lineno">1144</tt>  <tt class="py-line">            <tt class="py-keyword">for</tt> <tt class="py-name">c</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">counts</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt> <tt class="py-op">:</tt> <tt class="py-keyword">print</tt> <tt class="py-op">&gt;&gt;</tt><tt class="py-name">out</tt><tt class="py-op">,</tt> <tt class="py-name">c</tt><tt class="py-op">,</tt> <tt class="py-string">'\t'</tt><tt class="py-op">,</tt> </tt>
<a name="L1145"></a><tt class="py-lineno">1145</tt>  <tt class="py-line">            <tt class="py-keyword">print</tt> <tt class="py-op">&gt;&gt;</tt><tt class="py-name">out</tt><tt class="py-op">,</tt> <tt class="py-string">"%6.4f"</tt> <tt class="py-op">%</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">entropy</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-string">'\t'</tt><tt class="py-op">,</tt> </tt>
<a name="L1146"></a><tt class="py-lineno">1146</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">entropy_interval</tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L1147"></a><tt class="py-lineno">1147</tt>  <tt class="py-line">                <tt class="py-keyword">print</tt> <tt class="py-op">&gt;&gt;</tt><tt class="py-name">out</tt><tt class="py-op">,</tt> <tt class="py-string">"%6.4f"</tt> <tt class="py-op">%</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">entropy_interval</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-string">'\t'</tt><tt class="py-op">,</tt>  </tt>
<a name="L1148"></a><tt class="py-lineno">1148</tt>  <tt class="py-line">                <tt class="py-keyword">print</tt> <tt class="py-op">&gt;&gt;</tt><tt class="py-name">out</tt><tt class="py-op">,</tt> <tt class="py-string">"%6.4f"</tt> <tt class="py-op">%</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">entropy_interval</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-string">'\t'</tt><tt class="py-op">,</tt> </tt>
<a name="L1149"></a><tt class="py-lineno">1149</tt>  <tt class="py-line">            <tt class="py-keyword">else</tt> <tt class="py-op">:</tt> </tt>
<a name="L1150"></a><tt class="py-lineno">1150</tt>  <tt class="py-line">                <tt class="py-keyword">print</tt> <tt class="py-op">&gt;&gt;</tt><tt class="py-name">out</tt><tt class="py-op">,</tt> <tt class="py-string">'\t'</tt><tt class="py-op">,</tt><tt class="py-string">'\t'</tt><tt class="py-op">,</tt> </tt>
<a name="L1151"></a><tt class="py-lineno">1151</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">weight</tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</tt> <tt class="py-op">:</tt> </tt>
<a name="L1152"></a><tt class="py-lineno">1152</tt>  <tt class="py-line">                <tt class="py-keyword">print</tt> <tt class="py-op">&gt;&gt;</tt><tt class="py-name">out</tt><tt class="py-op">,</tt> <tt class="py-string">"%6.4f"</tt> <tt class="py-op">%</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">weight</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt>
<a name="L1153"></a><tt class="py-lineno">1153</tt>  <tt class="py-line">            <tt class="py-keyword">print</tt> <tt class="py-op">&gt;&gt;</tt><tt class="py-name">out</tt><tt class="py-op">,</tt> <tt class="py-string">''</tt> </tt>
<a name="L1154"></a><tt class="py-lineno">1154</tt>  <tt class="py-line">        <tt class="py-keyword">print</tt> <tt class="py-op">&gt;&gt;</tt><tt class="py-name">out</tt><tt class="py-op">,</tt> <tt class="py-string">'# End LogoData'</tt> </tt>
<a name="L1155"></a><tt class="py-lineno">1155</tt>  <tt class="py-line">         </tt>
<a name="L1156"></a><tt class="py-lineno">1156</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">out</tt><tt class="py-op">.</tt><tt class="py-name">getvalue</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L1157"></a><tt class="py-lineno">1157</tt>  <tt class="py-line"> </tt><script type="text/javascript">
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